ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge branch 'doc_fixes' of https://github.com/rbberger/lammps into collected-small-fixes

Browse Source
This commit is contained in:
Axel Kohlmeyer
2024-08-18 16:45:48 -04:00
parent e5876b3b36 84c102fe36
commit cac32085a7
43 changed files with 1310 additions and 969 deletions
Download Patch File Download Diff File Expand all files Collapse all files

84
doc/src/Build_basics.rst
View File

@ -37,8 +37,9 @@ standard. A more detailed discussion of that is below.
.. code-block:: bash .. code-block:: bash
-D BUILD_MPI=value # yes or no, default is yes if CMake finds MPI, else no -D BUILD_MPI=value # yes or no, default is yes if CMake finds MPI
-D BUILD_OMP=value # yes or no, default is yes if a compatible compiler is detected -D BUILD_OMP=value # yes or no, default is yes if a compatible
# compiler is detected
-D LAMMPS_MACHINE=name # name = mpi, serial, mybox, titan, laptop, etc -D LAMMPS_MACHINE=name # name = mpi, serial, mybox, titan, laptop, etc
# no default value # no default value
@ -54,9 +55,9 @@ standard. A more detailed discussion of that is below.
.. code-block:: bash .. code-block:: bash
make mpi # parallel build, produces lmp_mpi using Makefile.mpi make mpi # parallel build, produces lmp_mpi using Makefile.mpi
make serial # serial build, produces lmp_serial using Makefile/serial make serial # serial build, produces lmp_serial using Makefile/serial
make mybox # uses Makefile.mybox to produce lmp_mybox make mybox # uses Makefile.mybox to produce lmp_mybox
Any ``make machine`` command will look up the make settings from a Any ``make machine`` command will look up the make settings from a
file ``Makefile.machine`` in the folder ``src/MAKE`` or one of its file ``Makefile.machine`` in the folder ``src/MAKE`` or one of its
@ -74,15 +75,15 @@ standard. A more detailed discussion of that is below.
this is ``-fopenmp``\ , which can be added to the ``CC`` and this is ``-fopenmp``\ , which can be added to the ``CC`` and
``LINK`` makefile variables. ``LINK`` makefile variables.
For the serial build the following make variables are set (see src/MAKE/Makefile.serial): For the serial build the following make variables are set (see ``src/MAKE/Makefile.serial``):
.. code-block:: make .. code-block:: make
CC = g++ CC = g++
LINK = g++ LINK = g++
MPI_INC = -I../STUBS MPI_INC = -I../STUBS
MPI_PATH = -L../STUBS MPI_PATH = -L../STUBS
MPI_LIB = -lmpi_stubs MPI_LIB = -lmpi_stubs
You also need to build the STUBS library for your platform before You also need to build the STUBS library for your platform before
making LAMMPS itself. A ``make serial`` build does this for you making LAMMPS itself. A ``make serial`` build does this for you
@ -231,24 +232,32 @@ LAMMPS.
.. code-block:: bash .. code-block:: bash
# Building with GNU Compilers: # Building with GNU Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ \
-DCMAKE_Fortran_COMPILER=gfortran ../cmake
# Building with Intel Compilers: # Building with Intel Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc \
-DCMAKE_Fortran_COMPILER=ifort ../cmake
# Building with Intel oneAPI Compilers: # Building with Intel oneAPI Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx -DCMAKE_Fortran_COMPILER=ifx cmake -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx \
-DCMAKE_Fortran_COMPILER=ifx ../cmake
# Building with LLVM/Clang Compilers: # Building with LLVM/Clang Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ \
-DCMAKE_Fortran_COMPILER=flang ../cmake
# Building with PGI/Nvidia Compilers: # Building with PGI/Nvidia Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=pgcc -DCMAKE_CXX_COMPILER=pgc++ -DCMAKE_Fortran_COMPILER=pgfortran cmake -DCMAKE_C_COMPILER=pgcc -DCMAKE_CXX_COMPILER=pgc++ \
-DCMAKE_Fortran_COMPILER=pgfortran ../cmake
# Building with the NVHPC Compilers:
cmake -DCMAKE_C_COMPILER=nvc -DCMAKE_CXX_COMPILER=nvc++ \
-DCMAKE_Fortran_COMPILER=nvfortran ../cmake
For compiling with the Clang/LLVM compilers a CMake preset is For compiling with the Clang/LLVM compilers a CMake preset is
provided that can be loaded with provided that can be loaded with
`-C ../cmake/presets/clang.cmake`. Similarly, ``-C ../cmake/presets/clang.cmake``. Similarly,
`-C ../cmake/presets/intel.cmake` should switch the compiler ``-C ../cmake/presets/intel.cmake`` should switch the compiler
toolchain to the legacy Intel compilers, `-C ../cmake/presets/oneapi.cmake` toolchain to the legacy Intel compilers, ``-C ../cmake/presets/oneapi.cmake``
will switch to the LLVM based oneAPI Intel compilers, will switch to the LLVM based oneAPI Intel compilers,
and `-C ../cmake/presets/pgi.cmake` ``-C ../cmake/presets/pgi.cmake`` will switch the compiler to the PGI compilers,
will switch the compiler to the PGI compilers. and ``-C ../cmake/presets/nvhpc.cmake`` will switch to the NVHPC compilers.
Furthermore, you can set ``CMAKE_TUNE_FLAGS`` to specifically add Furthermore, you can set ``CMAKE_TUNE_FLAGS`` to specifically add
compiler flags to tune for optimal performance on given hosts. compiler flags to tune for optimal performance on given hosts.
@ -259,7 +268,7 @@ LAMMPS.
When the cmake command completes, it prints a summary to the When the cmake command completes, it prints a summary to the
screen which compilers it is using and what flags and settings screen which compilers it is using and what flags and settings
will be used for the compilation. Note that if the top-level will be used for the compilation. Note that if the top-level
compiler is mpicxx, it is simply a wrapper on a real compiler. compiler is ``mpicxx``, it is simply a wrapper on a real compiler.
The underlying compiler info is what CMake will try to The underlying compiler info is what CMake will try to
determine and report. You should check to confirm you are determine and report. You should check to confirm you are
using the compiler and optimization flags you want. using the compiler and optimization flags you want.
@ -278,19 +287,19 @@ LAMMPS.
.. code-block:: make .. code-block:: make
CC = mpicxx CC = mpicxx
CCFLAGS = -g -O3 CCFLAGS = -g -O3
LINK = mpicxx LINK = mpicxx
LINKFLAGS = -g -O LINKFLAGS = -g -O
Serial build with GNU gcc (see ``src/MAKE/Makefile.serial``): Serial build with GNU gcc (see ``src/MAKE/Makefile.serial``):
.. code-block:: make .. code-block:: make
CC = g++ CC = g++
CCFLAGS = -g -O3 CCFLAGS = -g -O3
LINK = g++ LINK = g++
LINKFLAGS = -g -O LINKFLAGS = -g -O
.. note:: .. note::
@ -316,10 +325,10 @@ LAMMPS.
there may be specific compiler or linker flags that are either there may be specific compiler or linker flags that are either
required or recommended to enable required features and to required or recommended to enable required features and to
achieve optimal performance. You need to include these in the achieve optimal performance. You need to include these in the
CCFLAGS and LINKFLAGS settings above. For details, see the ``CCFLAGS`` and ``LINKFLAGS`` settings above. For details, see the
documentation for the individual packages listed on the documentation for the individual packages listed on the
:doc:`Speed_packages` page. Or examine these files in the :doc:`Speed_packages` page. Or examine these files in the
src/MAKE/OPTIONS directory. They correspond to each of the 5 ``src/MAKE/OPTIONS`` directory. They correspond to each of the 5
accelerator packages and their hardware variants: accelerator packages and their hardware variants:
.. code-block:: bash .. code-block:: bash
@ -388,7 +397,8 @@ running LAMMPS from Python via its library interface.
make machine # build LAMMPS executable lmp_machine make machine # build LAMMPS executable lmp_machine
make mode=static machine # same as "make machine" make mode=static machine # same as "make machine"
make mode=shared machine # build LAMMPS shared lib liblammps_machine.so instead make mode=shared machine # build LAMMPS shared lib liblammps_machine.so
# instead
The "static" build will generate a static library called The "static" build will generate a static library called
``liblammps_machine.a`` and an executable named ``lmp_machine``\ , ``liblammps_machine.a`` and an executable named ``lmp_machine``\ ,
@ -450,7 +460,7 @@ installation.
Including or removing debug support Including or removing debug support
----------------------------------- -----------------------------------
By default the compilation settings will include the *-g* flag which By default the compilation settings will include the ``-g`` flag which
instructs the compiler to include debug information (e.g. which line of instructs the compiler to include debug information (e.g. which line of
source code a particular instruction correspond to). This can be source code a particular instruction correspond to). This can be
extremely useful in case LAMMPS crashes and can help to provide crucial extremely useful in case LAMMPS crashes and can help to provide crucial
@ -463,7 +473,7 @@ If this is a concern, you can change the compilation settings or remove
the debug information from the LAMMPS executable: the debug information from the LAMMPS executable:
- **Traditional make**: edit your ``Makefile.<machine>`` to remove the - **Traditional make**: edit your ``Makefile.<machine>`` to remove the
*-g* flag from the ``CCFLAGS`` and ``LINKFLAGS`` definitions ``-g`` flag from the ``CCFLAGS`` and ``LINKFLAGS`` definitions
- **CMake**: use ``-D CMAKE_BUILD_TYPE=Release`` or explicitly reset - **CMake**: use ``-D CMAKE_BUILD_TYPE=Release`` or explicitly reset
the applicable compiler flags (best done using the text mode or the applicable compiler flags (best done using the text mode or
graphical user interface). graphical user interface).
@ -488,7 +498,9 @@ using CMake or Make.
.. code-block:: bash .. code-block:: bash
-D BUILD_TOOLS=value # yes or no (default). Build binary2txt, chain.x, micelle2d.x, msi2lmp, phana, stl_bin2txt -D BUILD_TOOLS=value # yes or no (default). Build binary2txt,
# chain.x, micelle2d.x, msi2lmp, phana,
# stl_bin2txt
-D BUILD_LAMMPS_GUI=value # yes or no (default). Build LAMMPS-GUI -D BUILD_LAMMPS_GUI=value # yes or no (default). Build LAMMPS-GUI
The generated binaries will also become part of the LAMMPS installation The generated binaries will also become part of the LAMMPS installation

12
doc/src/Build_cmake.rst
View File

@ -131,20 +131,20 @@ file called ``CMakeLists.txt`` (for LAMMPS it is located in the
configuration step. The cache file contains all current CMake settings. configuration step. The cache file contains all current CMake settings.
To modify settings, enable or disable features, you need to set To modify settings, enable or disable features, you need to set
*variables* with either the *-D* command line flag (``-D *variables* with either the ``-D`` command line flag (``-D
VARIABLE1_NAME=value``) or change them in the text mode of the graphical VARIABLE1_NAME=value``) or change them in the text mode of the graphical
user interface. The *-D* flag can be used several times in one command. user interface. The ``-D`` flag can be used several times in one command.
For your convenience, we provide :ref:`CMake presets <cmake_presets>` For your convenience, we provide :ref:`CMake presets <cmake_presets>`
that combine multiple settings to enable optional LAMMPS packages or use that combine multiple settings to enable optional LAMMPS packages or use
a different compiler tool chain. Those are loaded with the *-C* flag a different compiler tool chain. Those are loaded with the ``-C`` flag
(``-C ../cmake/presets/basic.cmake``). This step would only be needed (``-C ../cmake/presets/basic.cmake``). This step would only be needed
once, as the settings from the preset files are stored in the once, as the settings from the preset files are stored in the
``CMakeCache.txt`` file. It is also possible to customize the build ``CMakeCache.txt`` file. It is also possible to customize the build
by adding one or more *-D* flags to the CMake command line. by adding one or more ``-D`` flags to the CMake command line.
Generating files for alternate build tools (e.g. Ninja) and project files Generating files for alternate build tools (e.g. Ninja) and project files
for IDEs like Eclipse, CodeBlocks, or Kate can be selected using the *-G* for IDEs like Eclipse, CodeBlocks, or Kate can be selected using the ``-G``
command line flag. A list of available generator settings for your command line flag. A list of available generator settings for your
specific CMake version is given when running ``cmake --help``. specific CMake version is given when running ``cmake --help``.
@ -171,7 +171,7 @@ files. E.g. with:
In that case the resulting binaries are not in the build folder directly In that case the resulting binaries are not in the build folder directly
but in subdirectories corresponding to the build type (i.e. Release in but in subdirectories corresponding to the build type (i.e. Release in
the example from above). Similarly, for running unit tests the the example from above). Similarly, for running unit tests the
configuration is selected with the *-C* flag: configuration is selected with the ``-C`` flag:
.. code-block:: bash .. code-block:: bash

98
doc/src/Build_development.rst
View File

@ -181,24 +181,24 @@ The output of this command will be looking something like this:
$ ctest $ ctest
Test project /home/akohlmey/compile/lammps/build-testing Test project /home/akohlmey/compile/lammps/build-testing
Start 1: RunLammps Start 1: RunLammps
1/563 Test #1: RunLammps .......................................... Passed 0.28 sec 1/563 Test #1: RunLammps .................................. Passed 0.28 sec
Start 2: HelpMessage Start 2: HelpMessage
2/563 Test #2: HelpMessage ........................................ Passed 0.06 sec 2/563 Test #2: HelpMessage ................................ Passed 0.06 sec
Start 3: InvalidFlag Start 3: InvalidFlag
3/563 Test #3: InvalidFlag ........................................ Passed 0.06 sec 3/563 Test #3: InvalidFlag ................................ Passed 0.06 sec
Start 4: Tokenizer Start 4: Tokenizer
4/563 Test #4: Tokenizer .......................................... Passed 0.05 sec 4/563 Test #4: Tokenizer .................................. Passed 0.05 sec
Start 5: MemPool Start 5: MemPool
5/563 Test #5: MemPool ............................................ Passed 0.05 sec 5/563 Test #5: MemPool .................................... Passed 0.05 sec
Start 6: ArgUtils Start 6: ArgUtils
6/563 Test #6: ArgUtils ........................................... Passed 0.05 sec 6/563 Test #6: ArgUtils ................................... Passed 0.05 sec
[...] [...]
Start 561: ImproperStyle:zero Start 561: ImproperStyle:zero
561/563 Test #561: ImproperStyle:zero ................................. Passed 0.07 sec 561/563 Test #561: ImproperStyle:zero ......................... Passed 0.07 sec
Start 562: TestMliapPyUnified Start 562: TestMliapPyUnified
562/563 Test #562: TestMliapPyUnified ................................. Passed 0.16 sec 562/563 Test #562: TestMliapPyUnified ......................... Passed 0.16 sec
Start 563: TestPairList Start 563: TestPairList
563/563 Test #563: TestPairList ....................................... Passed 0.06 sec 563/563 Test #563: TestPairList ............................... Passed 0.06 sec
100% tests passed, 0 tests failed out of 563 100% tests passed, 0 tests failed out of 563
@ -216,21 +216,21 @@ The ``ctest`` command has many options, the most important ones are:
* - Option * - Option
- Function - Function
* - -V * - ``-V``
- verbose output: display output of individual test runs - verbose output: display output of individual test runs
* - -j <num> * - ``-j <num>``
- parallel run: run <num> tests in parallel - parallel run: run <num> tests in parallel
* - -R <regex> * - ``-R <regex>``
- run subset of tests matching the regular expression <regex> - run subset of tests matching the regular expression <regex>
* - -E <regex> * - ``-E <regex>``
- exclude subset of tests matching the regular expression <regex> - exclude subset of tests matching the regular expression <regex>
* - -L <regex> * - ``-L <regex>``
- run subset of tests with a label matching the regular expression <regex> - run subset of tests with a label matching the regular expression <regex>
* - -LE <regex> * - ``-LE <regex>``
- exclude subset of tests with a label matching the regular expression <regex> - exclude subset of tests with a label matching the regular expression <regex>
* - -N * - ``-N``
- dry-run: display list of tests without running them - dry-run: display list of tests without running them
* - -T memcheck * - ``-T memcheck``
- run tests with valgrind memory checker (if available) - run tests with valgrind memory checker (if available)
In its full implementation, the unit test framework will consist of multiple In its full implementation, the unit test framework will consist of multiple
@ -339,13 +339,13 @@ The force style test programs have a common set of options:
* - Option * - Option
- Function - Function
* - -g <newfile> * - ``-g <newfile>``
- regenerate reference data in new YAML file - regenerate reference data in new YAML file
* - -u * - ``-u``
- update reference data in the original YAML file - update reference data in the original YAML file
* - -s * - ``-s``
- print error statistics for each group of comparisons - print error statistics for each group of comparisons
* - -v * - ``-v``
- verbose output: also print the executed LAMMPS commands - verbose output: also print the executed LAMMPS commands
The ``ctest`` tool has no mechanism to directly pass flags to the individual The ``ctest`` tool has no mechanism to directly pass flags to the individual
@ -359,10 +359,10 @@ set in an environment variable ``TEST_ARGS``. Example:
To add a test for a style that is not yet covered, it is usually best To add a test for a style that is not yet covered, it is usually best
to copy a YAML file for a similar style to a new file, edit the details to copy a YAML file for a similar style to a new file, edit the details
of the style (how to call it, how to set its coefficients) and then of the style (how to call it, how to set its coefficients) and then
run test command with either the *-g* and the replace the initial run test command with either the ``-g`` and the replace the initial
test file with the regenerated one or the *-u* option. The *-u* option test file with the regenerated one or the ``-u`` option. The ``-u`` option
will destroy the original file, if the generation run does not complete, will destroy the original file, if the generation run does not complete,
so using *-g* is recommended unless the YAML file is fully tested so using ``-g`` is recommended unless the YAML file is fully tested
and working. and working.
Some of the force style tests are rather slow to run and some are very Some of the force style tests are rather slow to run and some are very
@ -512,27 +512,51 @@ After post-processing with ``gen_coverage_html`` the results are in
a folder ``coverage_html`` and can be viewed with a web browser. a folder ``coverage_html`` and can be viewed with a web browser.
The images below illustrate how the data is presented. The images below illustrate how the data is presented.
.. list-table:: .. only:: not latex
* - .. figure:: JPG/coverage-overview-top.png .. list-table::
:scale: 25%
* - .. figure:: JPG/coverage-overview-top.png
:scale: 25%
Top of the overview page Top of the overview page
- .. figure:: JPG/coverage-overview-manybody.png - .. figure:: JPG/coverage-overview-manybody.png
:scale: 25% :scale: 25%
Styles with good coverage Styles with good coverage
- .. figure:: JPG/coverage-file-top.png - .. figure:: JPG/coverage-file-top.png
:scale: 25% :scale: 25%
Top of individual source page Top of individual source page
- .. figure:: JPG/coverage-file-branches.png - .. figure:: JPG/coverage-file-branches.png
:scale: 25% :scale: 25%
Source page with branches Source page with branches
.. only:: latex
.. figure:: JPG/coverage-overview-top.png
:width: 60%
Top of the overview page
.. figure:: JPG/coverage-overview-manybody.png
:width: 60%
Styles with good coverage
.. figure:: JPG/coverage-file-top.png
:width: 60%
Top of individual source page
.. figure:: JPG/coverage-file-branches.png
:width: 60%
Source page with branches
Coding style utilities Coding style utilities
---------------------- ----------------------

509
doc/src/Build_extras.rst
View File

@ -14,7 +14,7 @@ in addition to
cmake -D PKG_NAME=yes cmake -D PKG_NAME=yes
- .. code-block:: console - .. code-block:: bash
make yes-name make yes-name
@ -73,7 +73,7 @@ COMPRESS package
To build with this package you must have the `zlib compression library To build with this package you must have the `zlib compression library
<https://zlib.net>`_ available on your system to build dump styles with <https://zlib.net>`_ available on your system to build dump styles with
a '/gz' suffix. There are also styles using the a ``/gz`` suffix. There are also styles using the
`Zstandard <https://facebook.github.io/zstd/>`_ library which have a `Zstandard <https://facebook.github.io/zstd/>`_ library which have a
'/zstd' suffix. The zstd library version must be at least 1.4. Older '/zstd' suffix. The zstd library version must be at least 1.4. Older
versions use an incompatible API and thus LAMMPS will fail to compile. versions use an incompatible API and thus LAMMPS will fail to compile.
@ -95,7 +95,7 @@ versions use an incompatible API and thus LAMMPS will fail to compile.
<https://www.freedesktop.org/wiki/Software/pkg-config/>`_ tool to <https://www.freedesktop.org/wiki/Software/pkg-config/>`_ tool to
identify the necessary flags to compile with this library, so the identify the necessary flags to compile with this library, so the
corresponding ``libzstandard.pc`` file must be in a folder where corresponding ``libzstandard.pc`` file must be in a folder where
pkg-config can find it, which may require adding it to the ``pkg-config`` can find it, which may require adding it to the
``PKG_CONFIG_PATH`` environment variable. ``PKG_CONFIG_PATH`` environment variable.
.. tab:: Traditional make .. tab:: Traditional make
@ -127,46 +127,53 @@ CMake build
# value = double or mixed (default) or single # value = double or mixed (default) or single
-D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda -D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda
# value = sm_XX (see below, default is sm_50) # value = sm_XX (see below, default is sm_50)
-D GPU_DEBUG=value # enable debug code in the GPU package library, mostly useful for developers -D GPU_DEBUG=value # enable debug code in the GPU package library,
# mostly useful for developers
# value = yes or no (default) # value = yes or no (default)
-D HIP_PATH=value # value = path to HIP installation. Must be set if GPU_API=HIP -D HIP_PATH=value # value = path to HIP installation. Must be set if
# GPU_API=HIP
-D HIP_ARCH=value # primary GPU hardware choice for GPU_API=hip -D HIP_ARCH=value # primary GPU hardware choice for GPU_API=hip
# value depends on selected HIP_PLATFORM # value depends on selected HIP_PLATFORM
# default is 'gfx906' for HIP_PLATFORM=amd and 'sm_50' for HIP_PLATFORM=nvcc # default is 'gfx906' for HIP_PLATFORM=amd and 'sm_50' for
# HIP_PLATFORM=nvcc
-D HIP_USE_DEVICE_SORT=value # enables GPU sorting -D HIP_USE_DEVICE_SORT=value # enables GPU sorting
# value = yes (default) or no # value = yes (default) or no
-D CUDPP_OPT=value # use GPU binning on with CUDA (should be off for modern GPUs) -D CUDPP_OPT=value # use GPU binning with CUDA (should be off for modern GPUs)
# enables CUDA Performance Primitives, must be "no" for CUDA_MPS_SUPPORT=yes # enables CUDA Performance Primitives, must be "no" for
# CUDA_MPS_SUPPORT=yes
# value = yes or no (default) # value = yes or no (default)
-D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active nvidia-cuda-mps daemon -D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active
# nvidia-cuda-mps daemon
# value = yes or no (default) # value = yes or no (default)
-D CUDA_BUILD_MULTIARCH=value # enables building CUDA kernels for all supported GPU architectures -D CUDA_BUILD_MULTIARCH=value # enables building CUDA kernels for all supported GPU
# architectures
# value = yes (default) or no # value = yes (default) or no
-D USE_STATIC_OPENCL_LOADER=value # downloads/includes OpenCL ICD loader library, no local OpenCL headers/libs needed -D USE_STATIC_OPENCL_LOADER=value # downloads/includes OpenCL ICD loader library,
# no local OpenCL headers/libs needed
# value = yes (default) or no # value = yes (default) or no
:code:`GPU_ARCH` settings for different GPU hardware is as follows: ``GPU_ARCH`` settings for different GPU hardware is as follows:
* sm_30 for Kepler (supported since CUDA 5 and until CUDA 10.x) * ``sm_30`` for Kepler (supported since CUDA 5 and until CUDA 10.x)
* sm_35 or sm_37 for Kepler (supported since CUDA 5 and until CUDA 11.x) * ``sm_35`` or ``sm_37`` for Kepler (supported since CUDA 5 and until CUDA 11.x)
* sm_50 or sm_52 for Maxwell (supported since CUDA 6) * ``sm_50`` or ``sm_52`` for Maxwell (supported since CUDA 6)
* sm_60 or sm_61 for Pascal (supported since CUDA 8) * ``sm_60`` or ``sm_61`` for Pascal (supported since CUDA 8)
* sm_70 for Volta (supported since CUDA 9) * ``sm_70`` for Volta (supported since CUDA 9)
* sm_75 for Turing (supported since CUDA 10) * ``sm_75`` for Turing (supported since CUDA 10)
* sm_80 or sm_86 for Ampere (supported since CUDA 11, sm_86 since CUDA 11.1) * ``sm_80`` or sm_86 for Ampere (supported since CUDA 11, sm_86 since CUDA 11.1)
* sm_89 for Lovelace (supported since CUDA 11.8) * ``sm_89`` for Lovelace (supported since CUDA 11.8)
* sm_90 for Hopper (supported since CUDA 12.0) * ``sm_90`` for Hopper (supported since CUDA 12.0)
A more detailed list can be found, for example, A more detailed list can be found, for example,
at `Wikipedia's CUDA article <https://en.wikipedia.org/wiki/CUDA#GPUs_supported>`_ at `Wikipedia's CUDA article <https://en.wikipedia.org/wiki/CUDA#GPUs_supported>`_
CMake can detect which version of the CUDA toolkit is used and thus will CMake can detect which version of the CUDA toolkit is used and thus will
try to include support for **all** major GPU architectures supported by try to include support for **all** major GPU architectures supported by
this toolkit. Thus the GPU_ARCH setting is merely an optimization, to this toolkit. Thus the ``GPU_ARCH`` setting is merely an optimization, to
have code for the preferred GPU architecture directly included rather have code for the preferred GPU architecture directly included rather
than having to wait for the JIT compiler of the CUDA driver to translate than having to wait for the JIT compiler of the CUDA driver to translate
it. This behavior can be turned off (e.g. to speed up compilation) by it. This behavior can be turned off (e.g. to speed up compilation) by
setting :code:`CUDA_ENABLE_MULTIARCH` to :code:`no`. setting ``CUDA_ENABLE_MULTIARCH`` to ``no``.
When compiling for CUDA or HIP with CUDA, version 8.0 or later of the When compiling for CUDA or HIP with CUDA, version 8.0 or later of the
CUDA toolkit is required and a GPU architecture of Kepler or later, CUDA toolkit is required and a GPU architecture of Kepler or later,
@ -185,21 +192,21 @@ build, and link with a static OpenCL ICD loader library and standard
OpenCL headers. This way no local OpenCL development headers or library OpenCL headers. This way no local OpenCL development headers or library
needs to be present and only OpenCL compatible drivers need to be needs to be present and only OpenCL compatible drivers need to be
installed to use OpenCL. If this is not desired, you can set installed to use OpenCL. If this is not desired, you can set
:code:`USE_STATIC_OPENCL_LOADER` to :code:`no`. ``USE_STATIC_OPENCL_LOADER`` to ``no``.
The GPU library has some multi-thread support using OpenMP. If LAMMPS The GPU library has some multi-thread support using OpenMP. If LAMMPS
is built with ``-D BUILD_OMP=on`` this will also be enabled. is built with ``-D BUILD_OMP=on`` this will also be enabled.
If you are compiling with HIP, note that before running CMake you will If you are compiling with HIP, note that before running CMake you will
have to set appropriate environment variables. Some variables such as have to set appropriate environment variables. Some variables such as
:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are ``HCC_AMDGPU_TARGET`` (for ROCm <= 4.0) or ``CUDA_PATH`` are
necessary for :code:`hipcc` and the linker to work correctly. necessary for ``hipcc`` and the linker to work correctly.
.. versionadded:: 3Aug2022 .. versionadded:: 3Aug2022
Using the CHIP-SPV implementation of HIP is supported. It allows one to Using the CHIP-SPV implementation of HIP is supported. It allows one to
run HIP code on Intel GPUs via the OpenCL or Level Zero backends. To use run HIP code on Intel GPUs via the OpenCL or Level Zero backends. To use
CHIP-SPV, you must set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake CHIP-SPV, you must set ``-DHIP_USE_DEVICE_SORT=OFF`` in your CMake
command line as CHIP-SPV does not yet support hipCUB. As of Summer 2022, command line as CHIP-SPV does not yet support hipCUB. As of Summer 2022,
the use of HIP for Intel GPUs is experimental. You should only use this the use of HIP for Intel GPUs is experimental. You should only use this
option in preparations to run on Aurora system at Argonne. option in preparations to run on Aurora system at Argonne.
@ -257,28 +264,35 @@ script with the specified args:
.. code-block:: bash .. code-block:: bash
make lib-gpu # print help message # print help message
make lib-gpu args="-b" # build GPU library with default Makefile.linux make lib-gpu
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 # build GPU library with default Makefile.linux
make lib-gpu args="-b"
# create new Makefile.xk7.single, altered for single-precision
make lib-gpu args="-m xk7 -p single -o xk7.single"
# build GPU library with mixed precision and P100 using other settings in Makefile.mpi
make lib-gpu args="-m mpi -a sm_60 -p mixed -b"
Note that this procedure starts with a Makefile.machine in lib/gpu, as Note that this procedure starts with a Makefile.machine in lib/gpu, as
specified by the "-m" switch. For your convenience, machine makefiles specified by the ``-m`` switch. For your convenience, machine makefiles
for "mpi" and "serial" are provided, which have the same settings as for "mpi" and "serial" are provided, which have the same settings as
the corresponding machine makefiles in the main LAMMPS source the corresponding machine makefiles in the main LAMMPS source
folder. In addition you can alter 4 important settings in the folder. In addition you can alter 4 important settings in the
Makefile.machine you start from via the corresponding -c, -a, -p, -e Makefile.machine you start from via the corresponding ``-c``, ``-a``, ``-p``, ``-e``
switches (as in the examples above), and also save a copy of the new switches (as in the examples above), and also save a copy of the new
Makefile if desired: Makefile if desired:
* ``CUDA_HOME`` = where NVIDIA CUDA software is installed on your system * ``CUDA_HOME`` = where NVIDIA CUDA software is installed on your system
* ``CUDA_ARCH`` = sm_XX, what GPU hardware you have, same as CMake GPU_ARCH above * ``CUDA_ARCH`` = ``sm_XX``, what GPU hardware you have, same as CMake ``GPU_ARCH`` above
* ``CUDA_PRECISION`` = precision (double, mixed, single) * ``CUDA_PRECISION`` = precision (double, mixed, single)
* ``EXTRAMAKE`` = which Makefile.lammps.\* file to copy to Makefile.lammps * ``EXTRAMAKE`` = which ``Makefile.lammps.*`` file to copy to Makefile.lammps
The file Makefile.cuda is set up to include support for multiple The file ``Makefile.cuda`` is set up to include support for multiple
GPU architectures as supported by the CUDA toolkit in use. This is done GPU architectures as supported by the CUDA toolkit in use. This is done
through using the "--gencode " flag, which can be used multiple times and through using the ``--gencode`` flag, which can be used multiple times and
thus support all GPU architectures supported by your CUDA compiler. thus support all GPU architectures supported by your CUDA compiler.
To enable GPU binning via CUDA performance primitives set the Makefile variable To enable GPU binning via CUDA performance primitives set the Makefile variable
@ -349,12 +363,16 @@ minutes to hours) to build. Of course you only need to do that once.)
.. code-block:: bash .. code-block:: bash
-D DOWNLOAD_KIM=value # download OpenKIM API v2 for build, value = no (default) or yes -D DOWNLOAD_KIM=value # download OpenKIM API v2 for build
-D LMP_DEBUG_CURL=value # set libcurl verbose mode on/off, value = off (default) or on # value = no (default) or yes
-D LMP_NO_SSL_CHECK=value # tell libcurl to not verify the peer, value = no (default) or yes -D LMP_DEBUG_CURL=value # set libcurl verbose mode on/off
-D KIM_EXTRA_UNITTESTS=value # enables extra unit tests, value = no (default) or yes # value = off (default) or on
-D LMP_NO_SSL_CHECK=value # tell libcurl to not verify the peer
# value = no (default) or yes
-D KIM_EXTRA_UNITTESTS=value # enables extra unit tests
# value = no (default) or yes
If ``DOWNLOAD_KIM`` is set to *yes* (or *on*), the KIM API library If ``DOWNLOAD_KIM`` is set to ``yes`` (or ``on``), the KIM API library
will be downloaded and built inside the CMake build directory. If will be downloaded and built inside the CMake build directory. If
the KIM library is already installed on your system (in a location the KIM library is already installed on your system (in a location
where CMake cannot find it), you may need to set the where CMake cannot find it), you may need to set the
@ -362,7 +380,7 @@ minutes to hours) to build. Of course you only need to do that once.)
found, or run the command ``source kim-api-activate``. found, or run the command ``source kim-api-activate``.
Extra unit tests can only be available if they are explicitly requested Extra unit tests can only be available if they are explicitly requested
(``KIM_EXTRA_UNITTESTS`` is set to *yes* (or *on*)) and the prerequisites (``KIM_EXTRA_UNITTESTS`` is set to ``yes`` (or ``on``)) and the prerequisites
are met. See :ref:`KIM Extra unit tests <kim_extra_unittests>` for are met. See :ref:`KIM Extra unit tests <kim_extra_unittests>` for
more details on this. more details on this.
@ -376,15 +394,28 @@ minutes to hours) to build. Of course you only need to do that once.)
.. code-block:: bash .. code-block:: bash
make lib-kim # print help message # print help message
make lib-kim args="-b " # (re-)install KIM API lib with only example models make lib-kim
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
When using the "-b " option, the KIM library is built using its native # (re-)install KIM API lib with only example models
make lib-kim args="-b"
# ditto plus one model
make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"
# install KIM API lib with all models
make lib-kim args="-b -a everything"
# add one model or model driver
make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002"
# use an existing KIM API installation at the provided location
make lib-kim args="-p <prefix>"
# ditto but add one model or driver
make lib-kim args="-p <prefix> -a EAM_Dynamo_Ackland_W__MO_141627196590_002"
When using the ``-b`` option, the KIM library is built using its native
cmake build system. The ``lib/kim/Install.py`` script supports a cmake build system. The ``lib/kim/Install.py`` script supports a
``CMAKE`` environment variable if the cmake executable is named other ``CMAKE`` environment variable if the cmake executable is named other
than ``cmake`` on your system. Additional environment variables may be than ``cmake`` on your system. Additional environment variables may be
@ -394,7 +425,9 @@ minutes to hours) to build. Of course you only need to do that once.)
.. code-block:: bash .. code-block:: bash
CMAKE=cmake3 CXX=g++-11 CC=gcc-11 FC=gfortran-11 make lib-kim args="-b " # (re-)install KIM API lib using cmake3 and gnu v11 compilers with only example models # (re-)install KIM API lib using cmake3 and gnu v11 compilers
# with only example models
CMAKE=cmake3 CXX=g++-11 CC=gcc-11 FC=gfortran-11 make lib-kim args="-b"
Settings for debugging OpenKIM web queries discussed below need to Settings for debugging OpenKIM web queries discussed below need to
be applied by adding them to the ``LMP_INC`` variable through be applied by adding them to the ``LMP_INC`` variable through
@ -434,7 +467,7 @@ KIM Extra unit tests (CMake only)
During development, testing, or debugging, if During development, testing, or debugging, if
:doc:`unit testing <Build_development>` is enabled in LAMMPS, one can also :doc:`unit testing <Build_development>` is enabled in LAMMPS, one can also
enable extra tests on :doc:`KIM commands <kim_commands>` by setting the enable extra tests on :doc:`KIM commands <kim_commands>` by setting the
``KIM_EXTRA_UNITTESTS`` to *yes* (or *on*). ``KIM_EXTRA_UNITTESTS`` to ``yes`` (or ``on``).
Enabling the extra unit tests have some requirements, Enabling the extra unit tests have some requirements,
@ -449,10 +482,12 @@ Enabling the extra unit tests have some requirements,
*conda-forge* channel as ``conda install kim-property`` if LAMMPS is built in *conda-forge* channel as ``conda install kim-property`` if LAMMPS is built in
Conda. More detailed information is available at: Conda. More detailed information is available at:
`kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_. `kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
* It is also necessary to install * It is also necessary to install the following KIM models:
``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``,
``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``, and * ``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``
``LennardJones612_UniversalShifted__MO_959249795837_003`` KIM models. * ``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``
* ``LennardJones612_UniversalShifted__MO_959249795837_003``
See `Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_ See `Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_
to learn how to install a pre-built binary of the OpenKIM Repository of to learn how to install a pre-built binary of the OpenKIM Repository of
Models or see Models or see
@ -729,7 +764,8 @@ This list was last updated for version 4.3.0 of the Kokkos library.
mkdir build-kokkos-cuda mkdir build-kokkos-cuda
cd build-kokkos-cuda cd build-kokkos-cuda
cmake -C ../cmake/presets/basic.cmake -C ../cmake/presets/kokkos-cuda.cmake ../cmake cmake -C ../cmake/presets/basic.cmake \
-C ../cmake/presets/kokkos-cuda.cmake ../cmake
cmake --build . cmake --build .
.. tab:: Basic traditional make settings: .. tab:: Basic traditional make settings:
@ -757,9 +793,10 @@ This list was last updated for version 4.3.0 of the Kokkos library.
.. code-block:: make .. code-block:: make
KOKKOS_DEVICES = Cuda KOKKOS_DEVICES = Cuda
KOKKOS_ARCH = HOSTARCH,GPUARCH # HOSTARCH = HOST from list above that is hosting the GPU KOKKOS_ARCH = HOSTARCH,GPUARCH # HOSTARCH = HOST from list above that is
KOKKOS_CUDA_OPTIONS = "enable_lambda" # hosting the GPU
# GPUARCH = GPU from list above # GPUARCH = GPU from list above
KOKKOS_CUDA_OPTIONS = "enable_lambda"
FFT_INC = -DFFT_CUFFT # enable use of cuFFT (optional) FFT_INC = -DFFT_CUFFT # enable use of cuFFT (optional)
FFT_LIB = -lcufft # link to cuFFT library FFT_LIB = -lcufft # link to cuFFT library
@ -787,10 +824,11 @@ This list was last updated for version 4.3.0 of the Kokkos library.
.. code-block:: make .. code-block:: make
KOKKOS_DEVICES = HIP KOKKOS_DEVICES = HIP
KOKKOS_ARCH = HOSTARCH,GPUARCH # HOSTARCH = HOST from list above that is hosting the GPU KOKKOS_ARCH = HOSTARCH,GPUARCH # HOSTARCH = HOST from list above that is
# hosting the GPU
# GPUARCH = GPU from list above # GPUARCH = GPU from list above
FFT_INC = -DFFT_HIPFFT # enable use of hipFFT (optional) FFT_INC = -DFFT_HIPFFT # enable use of hipFFT (optional)
FFT_LIB = -lhipfft # link to hipFFT library FFT_LIB = -lhipfft # link to hipFFT library
Advanced KOKKOS compilation settings Advanced KOKKOS compilation settings
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -874,11 +912,16 @@ included in the LAMMPS source distribution in the ``lib/lepton`` folder.
.. code-block:: bash .. code-block:: bash
make lib-lepton # print help message # print help message
make lib-lepton args="-m serial" # build with GNU g++ compiler (settings as with "make serial") make lib-lepton
make lib-lepton args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
The "machine" argument of the "-m" flag is used to find a # build with GNU g++ compiler (settings as with "make serial")
make lib-lepton args="-m serial"
# build with default MPI compiler (settings as with "make mpi")
make lib-lepton args="-m mpi"
The "machine" argument of the ``-m`` flag is used to find a
Makefile.machine to use as build recipe. Makefile.machine to use as build recipe.
The build should produce a ``build`` folder and the library ``lib/lepton/liblmplepton.a`` The build should produce a ``build`` folder and the library ``lib/lepton/liblmplepton.a``
@ -900,7 +943,8 @@ Eigen3 is a template library, so you do not need to build it.
.. code-block:: bash .. code-block:: bash
-D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes -D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes
-D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a custom location) -D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a
# custom location)
If ``DOWNLOAD_EIGEN3`` is set, the Eigen3 library will be If ``DOWNLOAD_EIGEN3`` is set, the Eigen3 library will be
downloaded and inside the CMake build directory. If the Eigen3 downloaded and inside the CMake build directory. If the Eigen3
@ -918,9 +962,14 @@ Eigen3 is a template library, so you do not need to build it.
.. code-block:: bash .. code-block:: bash
make lib-machdyn # print help message # print help message
make lib-machdyn args="-b" # download to lib/machdyn/eigen3 make lib-machdyn
make lib-machdyn args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3
# download to lib/machdyn/eigen3
make lib-machdyn args="-b"
# use existing Eigen installation in /usr/include/eigen3
make lib-machdyn args="-p /usr/include/eigen3"
Note that a symbolic (soft) link named ``includelink`` is created Note that a symbolic (soft) link named ``includelink`` is created
in ``lib/machdyn`` to point to the Eigen dir. When LAMMPS builds it in ``lib/machdyn`` to point to the Eigen dir. When LAMMPS builds it
@ -994,7 +1043,7 @@ OPT package
The compiler flag ``-restrict`` must be used to build LAMMPS with The compiler flag ``-restrict`` must be used to build LAMMPS with
the OPT package when using Intel compilers. It should be added to the OPT package when using Intel compilers. It should be added to
the :code:`CCFLAGS` line of your ``Makefile.machine``. See the ``CCFLAGS`` line of your ``Makefile.machine``. See
``src/MAKE/OPTIONS/Makefile.opt`` for an example. ``src/MAKE/OPTIONS/Makefile.opt`` for an example.
---------- ----------
@ -1021,10 +1070,17 @@ POEMS package
.. code-block:: bash .. code-block:: bash
make lib-poems # print help message # print help message
make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial") make lib-poems
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 # build with GNU g++ compiler (settings as with "make serial")
make lib-poems args="-m serial"
# build with default MPI C++ compiler (settings as with "make mpi")
make lib-poems args="-m mpi"
# build with Intel icc compiler
make lib-poems args="-m icc"
The build should produce two files: ``lib/poems/libpoems.a`` and The build should produce two files: ``lib/poems/libpoems.a`` and
``lib/poems/Makefile.lammps``. The latter is copied from an ``lib/poems/Makefile.lammps``. The latter is copied from an
@ -1088,9 +1144,12 @@ binary package provided by your operating system.
.. code-block:: bash .. code-block:: bash
-D DOWNLOAD_VORO=value # download Voro++ for build, value = no (default) or yes -D DOWNLOAD_VORO=value # download Voro++ for build
-D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location) # value = no (default) or yes
-D VORO_INCLUDE_DIR=path # Voro++ include directory (only needed if at custom location) -D VORO_LIBRARY=path # Voro++ library file
# (only needed if at custom location)
-D VORO_INCLUDE_DIR=path # Voro++ include directory
# (only needed if at custom location)
If ``DOWNLOAD_VORO`` is set, the Voro++ library will be downloaded If ``DOWNLOAD_VORO`` is set, the Voro++ library will be downloaded
and built inside the CMake build directory. If the Voro++ library and built inside the CMake build directory. If the Voro++ library
@ -1110,12 +1169,19 @@ binary package provided by your operating system.
.. code-block:: bash .. code-block:: bash
make lib-voronoi # print help message # print help message
make lib-voronoi args="-b" # download and build the default version in lib/voronoi/voro++-<version> make lib-voronoi
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 # download and build the default version in lib/voronoi/voro++-<version>
make lib-voronoi args="-b"
# use existing Voro++ installation in $HOME/voro++
make lib-voronoi args="-p $HOME/voro++"
# download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
make lib-voronoi args="-b -v voro++0.4.6"
Note that two symbolic (soft) links, ``includelink`` and
``liblink``, are created in lib/voronoi to point to the Voro++ ``liblink``, are created in lib/voronoi to point to the Voro++
source dir. When LAMMPS builds in ``src`` it will use these source dir. When LAMMPS builds in ``src`` it will use these
links. You should not need to edit the links. You should not need to edit the
@ -1189,10 +1255,17 @@ The ATC package requires the MANYBODY package also be installed.
.. code-block:: bash .. code-block:: bash
make lib-atc # print help message # 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
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 # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-atc args="-m serial"
# build with default MPI compiler (settings as with "make mpi")
make lib-atc args="-m mpi"
# build with Intel icc compiler
make lib-atc args="-m icc"
The build should produce two files: ``lib/atc/libatc.a`` and The build should produce two files: ``lib/atc/libatc.a`` and
``lib/atc/Makefile.lammps``. The latter is copied from an ``lib/atc/Makefile.lammps``. The latter is copied from an
@ -1211,10 +1284,17 @@ The ATC package requires the MANYBODY package also be installed.
.. code-block:: bash .. code-block:: bash
make lib-linalg # print help message # print help message
make lib-linalg args="-m serial" # build with GNU C++ compiler (settings as with "make serial") make lib-linalg
make lib-linalg args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m g++" # build with GNU Fortran compiler # build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m serial"
# build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m mpi"
# build with GNU Fortran compiler
make lib-linalg args="-m g++"
---------- ----------
@ -1240,10 +1320,17 @@ AWPMD package
.. code-block:: bash .. code-block:: bash
make lib-awpmd # print help message # 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
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 # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-awpmd args="-m serial"
# build with default MPI compiler (settings as with "make mpi")
make lib-awpmd args="-m mpi"
# build with Intel icc compiler
make lib-awpmd args="-m icc"
The build should produce two files: ``lib/awpmd/libawpmd.a`` and The build should produce two files: ``lib/awpmd/libawpmd.a`` and
``lib/awpmd/Makefile.lammps``. The latter is copied from an ``lib/awpmd/Makefile.lammps``. The latter is copied from an
@ -1262,10 +1349,17 @@ AWPMD package
.. code-block:: bash .. code-block:: bash
make lib-linalg # print help message # print help message
make lib-linalg args="-m serial" # build with GNU C++ compiler (settings as with "make serial") make lib-linalg
make lib-linalg args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m g++" # build with GNU C++ compiler # build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m serial"
# build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m mpi"
# build with GNU C++ compiler
make lib-linalg args="-m g++"
---------- ----------
@ -1298,10 +1392,17 @@ module included in the LAMMPS source distribution.
.. code-block:: bash .. code-block:: bash
make lib-colvars # print help message # print help message
make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial") make lib-colvars
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 # build with GNU g++ compiler (settings as with "make serial")
make lib-colvars args="-m serial"
# build with default MPI compiler (settings as with "make mpi")
make lib-colvars args="-m mpi"
# build with GNU g++ compiler and colvars debugging enabled
make lib-colvars args="-m g++-debug"
The "machine" argument of the "-m" flag is used to find a The "machine" argument of the "-m" flag is used to find a
``Makefile.machine`` file to use as build recipe. If such recipe does ``Makefile.machine`` file to use as build recipe. If such recipe does
@ -1320,8 +1421,11 @@ module included in the LAMMPS source distribution.
.. code-block:: bash .. code-block:: bash
COLVARS_DEBUG=yes make lib-colvars args="-m machine" # Build with debug code (much slower) # Build with debug code (much slower)
COLVARS_LEPTON=no make lib-colvars args="-m machine" # Build without Lepton (included otherwise) COLVARS_DEBUG=yes make lib-colvars args="-m machine"
# Build without Lepton (included otherwise)
COLVARS_LEPTON=no make lib-colvars args="-m machine"
The build should produce two files: the library The build should produce two files: the library
``lib/colvars/libcolvars.a`` and the specification file ``lib/colvars/libcolvars.a`` and the specification file
@ -1368,9 +1472,14 @@ This package depends on the KSPACE package.
.. code-block:: bash .. code-block:: bash
make lib-electrode # print help message # print help message
make lib-electrode args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial") make lib-electrode
make lib-electrode args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
# build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-electrode args="-m serial"
# build with default MPI compiler (settings as with "make mpi")
make lib-electrode args="-m mpi"
Note that the ``Makefile.lammps`` file has settings for the BLAS Note that the ``Makefile.lammps`` file has settings for the BLAS
@ -1381,10 +1490,17 @@ This package depends on the KSPACE package.
.. code-block:: bash .. code-block:: bash
make lib-linalg # print help message # print help message
make lib-linalg args="-m serial" # build with GNU C++ compiler (settings as with "make serial") make lib-linalg
make lib-linalg args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m g++" # build with GNU C++ compiler # build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m serial"
# build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m mpi"
# build with GNU C++ compiler
make lib-linalg args="-m g++"
The package itself is activated with ``make yes-KSPACE`` and The package itself is activated with ``make yes-KSPACE`` and
``make yes-ELECTRODE`` ``make yes-ELECTRODE``
@ -1424,8 +1540,11 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
.. code-block:: bash .. code-block:: bash
make lib-pace # print help message # print help message
make lib-pace args="-b" # download and build the default version in lib/pace make lib-pace
# download and build the default version in lib/pace
make lib-pace args="-b"
You should not need to edit the ``lib/pace/Makefile.lammps`` file. You should not need to edit the ``lib/pace/Makefile.lammps`` file.
@ -1452,10 +1571,17 @@ ML-POD package
.. code-block:: bash .. code-block:: bash
make lib-mlpod # print help message # print help message
make lib-mlpod args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial") make lib-mlpod
make lib-mlpod args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
make lib-mlpod args="-m mpi -e linalg" # same as above but use the bundled linalg lib # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-mlpod args="-m serial"
# build with default MPI compiler (settings as with "make mpi")
make lib-mlpod args="-m mpi"
# same as above but use the bundled linalg lib
make lib-mlpod args="-m mpi -e linalg"
Note that the ``Makefile.lammps`` file has settings to use the BLAS Note that the ``Makefile.lammps`` file has settings to use the BLAS
and LAPACK linear algebra libraries. These can either exist on and LAPACK linear algebra libraries. These can either exist on
@ -1465,10 +1591,17 @@ ML-POD package
.. code-block:: bash .. code-block:: bash
make lib-linalg # print help message # print help message
make lib-linalg args="-m serial" # build with GNU C++ compiler (settings as with "make serial") make lib-linalg
make lib-linalg args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m g++" # build with GNU C++ compiler # build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m serial"
# build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m mpi"
# build with GNU C++ compiler
make lib-linalg args="-m g++"
The package itself is activated with ``make yes-ML-POD``. The package itself is activated with ``make yes-ML-POD``.
@ -1491,10 +1624,13 @@ within CMake will download the non-commercial use version.
.. code-block:: bash .. code-block:: bash
-D DOWNLOAD_QUIP=value # download QUIP library for build, value = no (default) or yes -D DOWNLOAD_QUIP=value # download QUIP library for build
-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location) # value = no (default) or yes
-D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK -D QUIP_LIBRARY=path # path to libquip.a
# value = no (default) or yes # (only needed if a custom location)
-D USE_INTERNAL_LINALG=value # Use the internal linear algebra library
# instead of LAPACK
# value = no (default) or yes
CMake will try to download and build the QUIP library from GitHub, CMake will try to download and build the QUIP library from GitHub,
if it is not found on the local machine. This requires to have git if it is not found on the local machine. This requires to have git
@ -1578,17 +1714,20 @@ LAMMPS build.
.. code-block:: bash .. code-block:: bash
-D DOWNLOAD_PLUMED=value # download PLUMED for build, value = no (default) or yes -D DOWNLOAD_PLUMED=value # download PLUMED for build
-D PLUMED_MODE=value # Linkage mode for PLUMED, value = static (default), shared, or runtime # value = no (default) or yes
-D PLUMED_MODE=value # Linkage mode for PLUMED
# value = static (default), shared,
# or runtime
If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be If ``DOWNLOAD_PLUMED`` is set to ``yes``, the PLUMED library will be
downloaded (the version of PLUMED that will be downloaded is downloaded (the version of PLUMED that will be downloaded is
hard-coded to a vetted version of PLUMED, usually a recent stable hard-coded to a vetted version of PLUMED, usually a recent stable
release version) and built inside the CMake build directory. If release version) and built inside the CMake build directory. If
``DOWNLOAD_PLUMED`` is set to "no" (the default), CMake will try ``DOWNLOAD_PLUMED`` is set to "no" (the default), CMake will try
to detect and link to an installed version of PLUMED. For this to to detect and link to an installed version of PLUMED. For this to
work, the PLUMED library has to be installed into a location where work, the PLUMED library has to be installed into a location where
the ``pkg-config`` tool can find it or the PKG_CONFIG_PATH the ``pkg-config`` tool can find it or the ``PKG_CONFIG_PATH``
environment variable has to be set up accordingly. PLUMED should environment variable has to be set up accordingly. PLUMED should
be installed in such a location if you compile it using the be installed in such a location if you compile it using the
default make; make install commands. default make; make install commands.
@ -1617,14 +1756,21 @@ LAMMPS build.
.. code-block:: bash .. code-block:: bash
make lib-plumed # print help message # print help message
make lib-plumed args="-b" # download and build PLUMED in lib/plumed/plumed2 make lib-plumed
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`` # download and build PLUMED in lib/plumed/plumed2
are created in lib/plumed that point to the location of the PLUMED make lib-plumed args="-b"
# use existing PLUMED installation in $HOME/.local
make lib-plumed args="-p $HOME/.local"
# use existing PLUMED installation in /usr/local and
# use shared linkage mode
make lib-plumed args="-p /usr/local -m shared"
Note that two symbolic (soft) links, ``includelink`` and ``liblink``
are created in ``lib/plumed`` that point to the location of the PLUMED
build to use. A new file ``lib/plumed/Makefile.lammps`` is also build to use. A new file ``lib/plumed/Makefile.lammps`` is also
created with settings suitable for LAMMPS to compile and link created with settings suitable for LAMMPS to compile and link
PLUMED using the desired linkage mode. After this step is PLUMED using the desired linkage mode. After this step is
@ -1639,17 +1785,17 @@ LAMMPS build.
Once this compilation completes you should be able to run LAMMPS Once this compilation completes you should be able to run LAMMPS
in the usual way. For shared linkage mode, libplumed.so must be in the usual way. For shared linkage mode, libplumed.so must be
found by the LAMMPS executable, which on many operating systems found by the LAMMPS executable, which on many operating systems
means, you have to set the LD_LIBRARY_PATH environment variable means, you have to set the ``LD_LIBRARY_PATH`` environment variable
accordingly. accordingly.
Support for the different linkage modes in LAMMPS varies for Support for the different linkage modes in LAMMPS varies for
different operating systems, using the static linkage is expected different operating systems, using the static linkage is expected
to be the most portable, and thus set to be the default. to be the most portable, and thus set to be the default.
If you want to change the linkage mode, you have to re-run "make If you want to change the linkage mode, you have to re-run ``make
lib-plumed" with the desired settings **and** do a re-install if lib-plumed`` with the desired settings **and** do a re-install if
the PLUMED package with "make yes-plumed" to update the the PLUMED package with ``make yes-plumed`` to update the
required makefile settings with the changes in the lib/plumed required makefile settings with the changes in the ``lib/plumed``
folder. folder.
---------- ----------
@ -1723,8 +1869,10 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
.. code-block:: bash .. code-block:: bash
-D DOWNLOAD_N2P2=value # download n2p2 for build, value = no (default) or yes -D DOWNLOAD_N2P2=value # download n2p2 for build
-D N2P2_DIR=path # n2p2 base directory (only needed if a custom location) # value = no (default) or yes
-D N2P2_DIR=path # n2p2 base directory
# (only needed if a custom location)
If ``DOWNLOAD_N2P2`` is set, the *n2p2* library will be downloaded and If ``DOWNLOAD_N2P2`` is set, the *n2p2* library will be downloaded and
built inside the CMake build directory. If the *n2p2* library is already built inside the CMake build directory. If the *n2p2* library is already
@ -1741,12 +1889,19 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
.. code-block:: bash .. code-block:: bash
make lib-hdnnp # print help message # print help message
make lib-hdnnp args="-b" # download and build in lib/hdnnp/n2p2-... make lib-hdnnp
make lib-hdnnp args="-b -v 2.1.4" # download and build specific version
make lib-hdnnp args="-p /usr/local/n2p2" # use the existing n2p2 installation in /usr/local/n2p2
Note that 3 symbolic (soft) links, ``includelink``, ``liblink`` and # download and build in lib/hdnnp/n2p2-...
make lib-hdnnp args="-b"
# download and build specific version
make lib-hdnnp args="-b -v 2.1.4"
# use the existing n2p2 installation in /usr/local/n2p2
make lib-hdnnp args="-p /usr/local/n2p2"
Note that three symbolic (soft) links, ``includelink``, ``liblink`` and
``Makefile.lammps``, will be created in ``lib/hdnnp`` to point to ``Makefile.lammps``, will be created in ``lib/hdnnp`` to point to
``n2p2/include``, ``n2p2/lib`` and ``n2p2/lib/Makefile.lammps-extra``, ``n2p2/include``, ``n2p2/lib`` and ``n2p2/lib/Makefile.lammps-extra``,
respectively. When LAMMPS is built in ``src`` it will use these links. respectively. When LAMMPS is built in ``src`` it will use these links.
@ -1793,19 +1948,19 @@ code when using features from the INTEL package.
.. code-block:: make .. code-block:: make
OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS) CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
LINKFLAGS = -g -qopenmp $(OPTFLAGS) LINKFLAGS = -g -qopenmp $(OPTFLAGS)
LIB = -ltbbmalloc LIB = -ltbbmalloc
For KNLs: For KNLs:
.. code-block:: make .. code-block:: make
OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS) CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
LINKFLAGS = -g -qopenmp $(OPTFLAGS) LINKFLAGS = -g -qopenmp $(OPTFLAGS)
LIB = -ltbbmalloc LIB = -ltbbmalloc
In Long-range thread mode (LRT) a modified verlet style is used, that In Long-range thread mode (LRT) a modified verlet style is used, that
operates the Kspace calculation in a separate thread concurrently to operates the Kspace calculation in a separate thread concurrently to
@ -1834,7 +1989,8 @@ MDI package
.. code-block:: bash .. code-block:: bash
-D DOWNLOAD_MDI=value # download MDI Library for build, value = no (default) or yes -D DOWNLOAD_MDI=value # download MDI Library for build
# value = no (default) or yes
.. tab:: Traditional make .. tab:: Traditional make
@ -1863,7 +2019,8 @@ MOLFILE package
.. code-block:: bash .. code-block:: bash
-D MOLFILE_INCLUDE_DIR=path # (optional) path where VMD molfile plugin headers are installed -D MOLFILE_INCLUDE_DIR=path # (optional) path where VMD molfile
# plugin headers are installed
-D PKG_MOLFILE=yes -D PKG_MOLFILE=yes
Using ``-D PKG_MOLFILE=yes`` enables the package, and setting Using ``-D PKG_MOLFILE=yes`` enables the package, and setting
@ -2022,10 +2179,17 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
.. code-block:: bash .. code-block:: bash
make lib-qmmm # print help message # print help message
make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial") make lib-qmmm
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 # build with GNU Fortran compiler (settings as in "make serial")
make lib-qmmm args="-m serial"
# build with default MPI compiler (settings as in "make mpi")
make lib-qmmm args="-m mpi"
# build with GNU Fortran compiler
make lib-qmmm args="-m gfortran"
The build should produce two files: ``lib/qmmm/libqmmm.a`` and The build should produce two files: ``lib/qmmm/libqmmm.a`` and
``lib/qmmm/Makefile.lammps``. The latter is copied from an ``lib/qmmm/Makefile.lammps``. The latter is copied from an
@ -2038,10 +2202,10 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
You can then install QMMM package and build LAMMPS in the usual You can then install QMMM package and build LAMMPS in the usual
manner. After completing the LAMMPS build and compiling Quantum manner. After completing the LAMMPS build and compiling Quantum
ESPRESSO with external library support (via "make couple"), go ESPRESSO with external library support (via ``make couple``), go
back to the ``lib/qmmm`` folder and follow the instructions in the back to the ``lib/qmmm`` folder and follow the instructions in the
README file to build the combined LAMMPS/QE QM/MM executable README file to build the combined LAMMPS/QE QM/MM executable
(pwqmmm.x) in the lib/qmmm folder. (``pwqmmm.x``) in the ``lib/qmmm`` folder.
---------- ----------
@ -2111,11 +2275,16 @@ To build with this package, you must download and build the
.. code-block:: bash .. code-block:: bash
make lib-scafacos # print help message # print help message
make lib-scafacos args="-b" # download and build in lib/scafacos/scafacos-<version> make lib-scafacos
make lib-scafacos args="-p $HOME/scafacos # use existing ScaFaCoS installation in $HOME/scafacos
Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``, are # download and build in lib/scafacos/scafacos-<version>
make lib-scafacos args="-b"
# use existing ScaFaCoS installation in $HOME/scafacos
make lib-scafacos args="-p $HOME/scafacos
Note that two symbolic (soft) links, ``includelink`` and ``liblink``, are
created in ``lib/scafacos`` to point to the ScaFaCoS src dir. When LAMMPS created in ``lib/scafacos`` to point to the ScaFaCoS src dir. When LAMMPS
builds in src it will use these links. You should not need to edit builds in src it will use these links. You should not need to edit
the ``lib/scafacos/Makefile.lammps`` file. the ``lib/scafacos/Makefile.lammps`` file.

10
doc/src/Build_link.rst
View File

@ -37,7 +37,7 @@ executable code from the library is copied into the calling executable.
.. tab:: CMake build .. tab:: CMake build
This assumes that LAMMPS has been configured without setting a This assumes that LAMMPS has been configured without setting a
``LAMMPS_MACHINE`` name, installed with "make install", and the ``LAMMPS_MACHINE`` name, installed with ``make install``, and the
``PKG_CONFIG_PATH`` environment variable has been updated to ``PKG_CONFIG_PATH`` environment variable has been updated to
include the ``liblammps.pc`` file installed into the configured include the ``liblammps.pc`` file installed into the configured
destination folder. The commands to compile and link a coupled destination folder. The commands to compile and link a coupled
@ -59,10 +59,10 @@ executable code from the library is copied into the calling executable.
mpicc -c -O -I${HOME}/lammps/src caller.c mpicc -c -O -I${HOME}/lammps/src caller.c
mpicxx -o caller caller.o -L${HOME}/lammps/src -llammps_mpi mpicxx -o caller caller.o -L${HOME}/lammps/src -llammps_mpi
The *-I* argument is the path to the location of the ``library.h`` The ``-I`` argument is the path to the location of the ``library.h``
header file containing the interface to the LAMMPS C-style library header file containing the interface to the LAMMPS C-style library
interface. The *-L* argument is the path to where the interface. The ``-L`` argument is the path to where the
``liblammps_mpi.a`` file is located. The *-llammps_mpi* argument ``liblammps_mpi.a`` file is located. The ``-llammps_mpi`` argument
is shorthand for telling the compiler to link the file is shorthand for telling the compiler to link the file
``liblammps_mpi.a``. If LAMMPS has been built as a shared ``liblammps_mpi.a``. If LAMMPS has been built as a shared
library, then the linker will use ``liblammps_mpi.so`` instead. library, then the linker will use ``liblammps_mpi.so`` instead.
@ -142,7 +142,7 @@ When linking to LAMMPS built as a shared library, the situation becomes
much simpler, as all dependent libraries and objects are either included much simpler, as all dependent libraries and objects are either included
in the shared library or registered as a dependent library in the shared in the shared library or registered as a dependent library in the shared
library file. Thus, those libraries need not be specified when linking library file. Thus, those libraries need not be specified when linking
the calling executable. Only the *-I* flags are needed. So the example the calling executable. Only the ``-I`` flags are needed. So the example
case from above of the serial version static LAMMPS library with the case from above of the serial version static LAMMPS library with the
POEMS package installed becomes: POEMS package installed becomes:

2
doc/src/Build_make.rst
View File

@ -25,7 +25,7 @@ additional tools to be available and functioning.
require adding flags like ``-std=c++11`` to enable the C++11 mode. require adding flags like ``-std=c++11`` to enable the C++11 mode.
* A Bourne shell compatible "Unix" shell program (frequently this is ``bash``) * A Bourne shell compatible "Unix" shell program (frequently this is ``bash``)
* A few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname`` * A few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
* Python (optional, required for ``make lib-<pkg>`` in the src * Python (optional, required for ``make lib-<pkg>`` in the ``src``
folder). Python scripts are currently tested with python 2.7 and folder). Python scripts are currently tested with python 2.7 and
3.6 to 3.11. The procedure for :doc:`building the documentation 3.6 to 3.11. The procedure for :doc:`building the documentation
<Build_manual>` *requires* Python 3.5 or later. <Build_manual>` *requires* Python 3.5 or later.

58
doc/src/Build_package.rst
View File

@ -100,10 +100,10 @@ versus make.
.. code-block:: bash .. code-block:: bash
cd lammps/src cd lammps/src
make ps # check which packages are currently installed make ps # check which packages are currently installed
make yes-name # install a package with name make yes-name # install a package with name
make no-name # uninstall a package with name make no-name # uninstall a package with name
make mpi # build LAMMPS with whatever packages are now installed make mpi # build LAMMPS with whatever packages are now installed
Examples: Examples:
@ -172,18 +172,41 @@ make a copy of one of them and modify it to suit your needs.
.. code-block:: bash .. code-block:: bash
cmake -C ../cmake/presets/basic.cmake [OPTIONS] ../cmake # enable just a few core packages # enable just a few core packages
cmake -C ../cmake/presets/most.cmake [OPTIONS] ../cmake # enable most packages cmake -C ../cmake/presets/basic.cmake [OPTIONS] ../cmake
cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake # enable packages which download sources or potential files
cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake # disable packages that do require extra libraries or tools # enable most packages
cmake -C ../cmake/presets/clang.cmake [OPTIONS] ../cmake # change settings to use the Clang compilers by default cmake -C ../cmake/presets/most.cmake [OPTIONS] ../cmake
cmake -C ../cmake/presets/gcc.cmake [OPTIONS] ../cmake # change settings to use the GNU compilers by default
cmake -C ../cmake/presets/intel.cmake [OPTIONS] ../cmake # change settings to use the Intel compilers by default # enable packages which download sources or potential files
cmake -C ../cmake/presets/pgi.cmake [OPTIONS] ../cmake # change settings to use the PGI compilers by default cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake
cmake -C ../cmake/presets/all_on.cmake [OPTIONS] ../cmake # enable all packages
cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake # disable all packages # disable packages that do require extra libraries or tools
mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake # compile with MinGW cross-compilers cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake
cmake -C ../cmake/presets/macos-multiarch.cmake [OPTIONS] ../cmake # compile serial multi-arch binaries on macOS
# change settings to use the Clang compilers by default
cmake -C ../cmake/presets/clang.cmake [OPTIONS] ../cmake
# change settings to use the GNU compilers by default
cmake -C ../cmake/presets/gcc.cmake [OPTIONS] ../cmake
# change settings to use the Intel compilers by default
cmake -C ../cmake/presets/intel.cmake [OPTIONS] ../cmake
# change settings to use the PGI compilers by default
cmake -C ../cmake/presets/pgi.cmake [OPTIONS] ../cmake
# enable all packages
cmake -C ../cmake/presets/all_on.cmake [OPTIONS] ../cmake
# disable all packages
cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake
# compile with MinGW cross-compilers
mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake
# compile serial multi-arch binaries on macOS
cmake -C ../cmake/presets/macos-multiarch.cmake [OPTIONS] ../cmake
Presets that have names starting with "windows" are specifically for Presets that have names starting with "windows" are specifically for
compiling LAMMPS :doc:`natively on Windows <Build_windows>` and compiling LAMMPS :doc:`natively on Windows <Build_windows>` and
@ -209,7 +232,8 @@ Example
# GPU package and configure it for using CUDA. You can run. # GPU package and configure it for using CUDA. You can run.
mkdir build mkdir build
cd build cd build
cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on -D GPU_API=cuda ../cmake cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake \
-D PKG_GPU=on -D GPU_API=cuda ../cmake
# to add another package, say BODY to the previous configuration you can run: # to add another package, say BODY to the previous configuration you can run:
cmake -D PKG_BODY=on . cmake -D PKG_BODY=on .

146
doc/src/Build_settings.rst
View File

@ -1,3 +1,7 @@
.. raw:: latex
\clearpage
Optional build settings Optional build settings
======================= =======================
@ -54,7 +58,7 @@ LAMMPS can use them if they are available on your system.
Alternatively, LAMMPS can use the `heFFTe Alternatively, LAMMPS can use the `heFFTe
<https://icl-utk-edu.github.io/heffte/>`_ library for the MPI <https://icl-utk-edu.github.io/heffte/>`_ library for the MPI
communication algorithms, which comes with many optimizations for communication algorithms, which comes with many optimizations for
special cases, e.g. leveraging available 2D and 3D FFTs in the back end special cases, e.g. leveraging available 2D and 3D FFTs in the backend
libraries and better pipelining for packing and communication. libraries and better pipelining for packing and communication.
.. tabs:: .. tabs::
@ -63,8 +67,10 @@ libraries and better pipelining for packing and communication.
.. code-block:: bash .. code-block:: bash
-D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS -D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found,
-D FFT_KOKKOS=value # FFTW3 or MKL or KISS or CUFFT or HIPFFT, default is KISS # else KISS
-D FFT_KOKKOS=value # FFTW3 or MKL or KISS or CUFFT or HIPFFT,
# default is KISS
-D FFT_SINGLE=value # yes or no (default), no = double precision -D FFT_SINGLE=value # yes or no (default), no = double precision
-D FFT_PACK=value # array (default) or pointer or memcpy -D FFT_PACK=value # array (default) or pointer or memcpy
-D FFT_USE_HEFFTE=value # yes or no (default), yes links to heFFTe -D FFT_USE_HEFFTE=value # yes or no (default), yes links to heFFTe
@ -72,11 +78,11 @@ libraries and better pipelining for packing and communication.
.. note:: .. note::
When the Kokkos variant of a package is compiled and selected at run time, When the Kokkos variant of a package is compiled and selected at run time,
the FFT library selected by the FFT_KOKKOS variable applies. Otherwise, the FFT library selected by the ``FFT_KOKKOS`` variable applies. Otherwise,
the FFT library selected by the FFT variable applies. the FFT library selected by the FFT variable applies.
The same FFT settings apply to both. FFT_KOKKOS must be compatible with the The same FFT settings apply to both. ``FFT_KOKKOS`` must be compatible with the
Kokkos back end - for example, when using the CUDA back end of Kokkos, Kokkos backend - for example, when using the CUDA backend of Kokkos,
you must use either CUFFT or KISS. you must use either ``CUFFT`` or ``KISS``.
Usually these settings are all that is needed. If FFTW3 is Usually these settings are all that is needed. If FFTW3 is
selected, then CMake will try to detect, if threaded FFTW selected, then CMake will try to detect, if threaded FFTW
@ -94,12 +100,13 @@ libraries and better pipelining for packing and communication.
-D MKL_INCLUDE_DIR=path # ditto for Intel MKL library -D MKL_INCLUDE_DIR=path # ditto for Intel MKL library
-D FFT_MKL_THREADS=on # enable using threaded FFTs with MKL libraries -D FFT_MKL_THREADS=on # enable using threaded FFTs with MKL libraries
-D MKL_LIBRARY=path # path to MKL libraries -D MKL_LIBRARY=path # path to MKL libraries
-D FFT_HEFFTE_BACKEND=value # FFTW or MKL or empty/undefined for the stock heFFTe back end -D FFT_HEFFTE_BACKEND=value # FFTW or MKL or empty/undefined for the stock
# heFFTe backend
-D Heffte_ROOT=path # path to an existing heFFTe installation -D Heffte_ROOT=path # path to an existing heFFTe installation
.. note:: .. note::
heFFTe comes with a builtin (= stock) back end for FFTs, i.e. a heFFTe comes with a builtin (= stock) backend for FFTs, i.e. a
default internal FFT implementation; however, this stock back default internal FFT implementation; however, this stock back
end is intended for testing purposes only and is not optimized end is intended for testing purposes only and is not optimized
for production runs. for production runs.
@ -113,30 +120,50 @@ libraries and better pipelining for packing and communication.
.. code-block:: make .. code-block:: make
FFT_INC = -DFFT_FFTW3 # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS FFT_INC = -DFFT_<NAME> # where <NAME> is KISS (default), FFTW3,
# default is KISS if not specified # FFTW (same as FFTW3), or MKL
FFT_INC = -DFFT_KOKKOS_CUFFT # -DFFT_KOKKOS_{FFTW,FFTW3,MKL,CUFFT,HIPFFT,KISS} FFT_INC = -DFFT_KOKKOS_<NAME> # where <NAME> is KISS (default), FFTW3,
# default is KISS if not specified # FFTW (same as FFTW3), MKL, CUFFT, or HIPFFT
FFT_INC = -DFFT_SINGLE # do not specify for double precision FFT_INC = -DFFT_SINGLE # do not specify for double precision
FFT_INC = -DFFT_FFTW_THREADS # enable using threaded FFTW3 libraries FFT_INC = -DFFT_FFTW_THREADS # enable using threaded FFTW3 libraries
FFT_INC = -DFFT_MKL_THREADS # enable using threaded FFTs with MKL libraries FFT_INC = -DFFT_MKL_THREADS # enable using threaded FFTs with MKL libraries
FFT_INC = -DFFT_PACK_ARRAY # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY FFT_INC = -DFFT_PACK_ARRAY # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
# default is FFT_PACK_ARRAY if not specified # default is FFT_PACK_ARRAY if not specified
.. code-block:: make .. code-block:: make
FFT_INC = -I/usr/local/include FFT_INC = -I/usr/local/include
FFT_PATH = -L/usr/local/lib FFT_PATH = -L/usr/local/lib
FFT_LIB = -lhipfft # hipFFT either precision
FFT_LIB = -lcufft # cuFFT either precision # hipFFT either precision
FFT_LIB = -lfftw3 # FFTW3 double precision FFT_LIB = -lhipfft
FFT_LIB = -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
FFT_LIB = -lfftw3 -lfftw3f # FFTW3 single precision # cuFFT either precision
FFT_LIB = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core # MKL with Intel compiler, serial interface FFT_LIB = -lcufft
FFT_LIB = -lmkl_gf_lp64 -lmkl_sequential -lmkl_core # MKL with GNU compiler, serial interface
FFT_LIB = -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core # MKL with Intel compiler, threaded interface # FFTW3 double precision
FFT_LIB = -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core # MKL with GNU compiler, threaded interface FFT_LIB = -lfftw3
FFT_LIB = -lmkl_rt # MKL with automatic runtime selection of interface libs
# FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
FFT_LIB = -lfftw3 -lfftw3_omp
# FFTW3 single precision
FFT_LIB = -lfftw3 -lfftw3f
# serial MKL with Intel compiler
FFT_LIB = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
# serial MKL with GNU compiler
FFT_LIB = -lmkl_gf_lp64 -lmkl_sequential -lmkl_core
# threaded MKL with Intel compiler
FFT_LIB = -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core
# threaded MKL with GNU compiler
FFT_LIB = -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core
# MKL with automatic runtime selection of interface libs
FFT_LIB = -lmkl_rt
As with CMake, you do not need to set paths in ``FFT_INC`` or As with CMake, you do not need to set paths in ``FFT_INC`` or
``FFT_PATH``, if the compiler can find the FFT header and library ``FFT_PATH``, if the compiler can find the FFT header and library
@ -152,13 +179,13 @@ libraries and better pipelining for packing and communication.
FFT_PATH = FFT_PATH =
FFT_LIB = $(heffte_link) $(heffte_libs) FFT_LIB = $(heffte_link) $(heffte_libs)
The heFFTe install path will contain `HeffteMakefile.in`. The heFFTe install path will contain ``HeffteMakefile.in``.
which will define the `heffte_` include variables needed to link to heFFTe from which will define the ``heffte_`` include variables needed to link to heFFTe from
an external project using traditional make. an external project using traditional make.
The `-DFFT_HEFFTE` is required to switch to using heFFTe, while the optional `-DFFT_HEFFTE_FFTW` The ``-DFFT_HEFFTE`` is required to switch to using heFFTe, while the optional ``-DFFT_HEFFTE_FFTW``
selects the desired heFFTe back end, e.g., `-DFFT_HEFFTE_FFTW` or `-DFFT_HEFFTE_MKL`, selects the desired heFFTe backend, e.g., ``-DFFT_HEFFTE_FFTW`` or ``-DFFT_HEFFTE_MKL``,
omitting the variable will default to the `stock` back end. omitting the variable will default to the `stock` backend.
The heFFTe `stock` back end is intended to be used for testing and debugging, The heFFTe `stock` backend is intended to be used for testing and debugging,
but is not performance optimized for large scale production runs. but is not performance optimized for large scale production runs.
The `KISS FFT library <https://github.com/mborgerding/kissfft>`_ is The `KISS FFT library <https://github.com/mborgerding/kissfft>`_ is
@ -184,7 +211,7 @@ it from `www.fftw.org <https://www.fftw.org>`_. LAMMPS requires version
Building FFTW for your box should be as simple as ``./configure; make; Building FFTW for your box should be as simple as ``./configure; make;
make install``. The install command typically requires root privileges make install``. The install command typically requires root privileges
(e.g. invoke it via sudo), unless you specify a local directory with (e.g. invoke it via sudo), unless you specify a local directory with
the "--prefix" option of configure. Type ``./configure --help`` to see the ``--prefix`` option of configure. Type ``./configure --help`` to see
various options. various options.
The Intel MKL math library is part of the Intel compiler suite. It The Intel MKL math library is part of the Intel compiler suite. It
@ -193,7 +220,7 @@ above).
The cuFFT and hipFFT FFT libraries are packaged with NVIDIA's CUDA and The cuFFT and hipFFT FFT libraries are packaged with NVIDIA's CUDA and
AMD's HIP installations, respectively. These FFT libraries require the AMD's HIP installations, respectively. These FFT libraries require the
Kokkos acceleration package to be enabled and the Kokkos back end to be Kokkos acceleration package to be enabled and the Kokkos backend to be
GPU-resident (i.e., HIP or CUDA). GPU-resident (i.e., HIP or CUDA).
Performing 3d FFTs in parallel can be time-consuming due to data access Performing 3d FFTs in parallel can be time-consuming due to data access
@ -220,7 +247,7 @@ produce the additional libraries ``libfftw3f.a`` and/or ``libfftw3f.so``\ .
Performing 3d FFTs requires communication to transpose the 3d FFT Performing 3d FFTs requires communication to transpose the 3d FFT
grid. The data packing/unpacking for this can be done in one of 3 grid. The data packing/unpacking for this can be done in one of 3
modes (ARRAY, POINTER, MEMCPY) as set by the FFT_PACK syntax above. modes (ARRAY, POINTER, MEMCPY) as set by the ``FFT_PACK`` syntax above.
Depending on the machine, the size of the FFT grid, the number of Depending on the machine, the size of the FFT grid, the number of
processors used, one option may be slightly faster. The default is processors used, one option may be slightly faster. The default is
ARRAY mode. ARRAY mode.
@ -228,7 +255,7 @@ ARRAY mode.
When using ``-DFFT_HEFFTE`` CMake will first look for an existing When using ``-DFFT_HEFFTE`` CMake will first look for an existing
install with hints provided by ``-DHeffte_ROOT``, as recommended by the install with hints provided by ``-DHeffte_ROOT``, as recommended by the
CMake standard and note that the name is case sensitive. If CMake cannot CMake standard and note that the name is case sensitive. If CMake cannot
find a heFFTe installation with the correct back end (e.g., FFTW or find a heFFTe installation with the correct backend (e.g., FFTW or
MKL), it will attempt to download and build the library automatically. MKL), it will attempt to download and build the library automatically.
In this case, LAMMPS CMake will also accept all heFFTe specific In this case, LAMMPS CMake will also accept all heFFTe specific
variables listed in the `heFFTe documentation variables listed in the `heFFTe documentation
@ -237,6 +264,10 @@ and those variables will be passed into the heFFTe build.
---------- ----------
.. raw:: latex
\clearpage
.. _size: .. _size:
Size of LAMMPS integer types and size limits Size of LAMMPS integer types and size limits
@ -360,12 +391,13 @@ requires the following settings:
.. code-block:: bash .. code-block:: bash
-D WITH_JPEG=value # yes or no -D WITH_JPEG=value # yes or no
# default = yes if CMake finds JPEG development files, else no # default = yes if CMake finds JPEG development files, else no
-D WITH_PNG=value # yes or no -D WITH_PNG=value # yes or no
# default = yes if CMake finds PNG and ZLIB development files, else no # default = yes if CMake finds PNG and ZLIB development files,
-D WITH_FFMPEG=value # yes or no # else no
# default = yes if CMake can find ffmpeg, else no -D WITH_FFMPEG=value # yes or no
# default = yes if CMake can find ffmpeg, else no
Usually these settings are all that is needed. If CMake cannot Usually these settings are all that is needed. If CMake cannot
find the graphics header, library, executable files, you can set find the graphics header, library, executable files, you can set
@ -387,8 +419,10 @@ requires the following settings:
LMP_INC = -DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG <other LMP_INC settings> LMP_INC = -DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG <other LMP_INC settings>
JPG_INC = -I/usr/local/include # path to jpeglib.h, png.h, zlib.h header files if make cannot find them JPG_INC = -I/usr/local/include # path to jpeglib.h, png.h, zlib.h headers
JPG_PATH = -L/usr/lib # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them # if make cannot find them
JPG_PATH = -L/usr/lib # paths to libjpeg.a, libpng.a, libz.a (.so)
# files if make cannot find them
JPG_LIB = -ljpeg -lpng -lz # library names JPG_LIB = -ljpeg -lpng -lz # library names
As with CMake, you do not need to set ``JPG_INC`` or ``JPG_PATH``, As with CMake, you do not need to set ``JPG_INC`` or ``JPG_PATH``,
@ -428,8 +462,8 @@ including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
.. code-block:: bash .. code-block:: bash
-D WITH_GZIP=value # yes or no -D WITH_GZIP=value # yes or no
# default is yes if CMake can find the gzip program, else no # default is yes if CMake can find the gzip program
.. tab:: Traditional make .. tab:: Traditional make
@ -504,11 +538,11 @@ LAMMPS is compiled accordingly which needs the following settings:
Memory allocation alignment Memory allocation alignment
--------------------------- ---------------------------
This setting enables the use of the "posix_memalign()" call instead of This setting enables the use of the ``posix_memalign()`` call instead of
"malloc()" when LAMMPS allocates large chunks of memory. Vector ``malloc()`` when LAMMPS allocates large chunks of memory. Vector
instructions on CPUs may become more efficient, if dynamically allocated instructions on CPUs may become more efficient, if dynamically allocated
memory is aligned on larger-than-default byte boundaries. On most memory is aligned on larger-than-default byte boundaries. On most
current operating systems, the "malloc()" implementation returns current operating systems, the ``malloc()`` implementation returns
pointers that are aligned to 16-byte boundaries. Using SSE vector pointers that are aligned to 16-byte boundaries. Using SSE vector
instructions efficiently, however, requires memory blocks being aligned instructions efficiently, however, requires memory blocks being aligned
on 64-byte boundaries. on 64-byte boundaries.
@ -522,9 +556,9 @@ on 64-byte boundaries.
-D LAMMPS_MEMALIGN=value # 0, 8, 16, 32, 64 (default) -D LAMMPS_MEMALIGN=value # 0, 8, 16, 32, 64 (default)
Use a ``LAMMPS_MEMALIGN`` value of 0 to disable using Use a ``LAMMPS_MEMALIGN`` value of 0 to disable using
"posix_memalign()" and revert to using the "malloc()" C-library ``posix_memalign()`` and revert to using the ``malloc()`` C-library
function instead. When compiling LAMMPS for Windows systems, function instead. When compiling LAMMPS for Windows systems,
"malloc()" will always be used and this setting is ignored. ``malloc()`` will always be used and this setting is ignored.
.. tab:: Traditional make .. tab:: Traditional make
@ -533,7 +567,7 @@ on 64-byte boundaries.
LMP_INC = -DLAMMPS_MEMALIGN=value # 8, 16, 32, 64 LMP_INC = -DLAMMPS_MEMALIGN=value # 8, 16, 32, 64
Do not set ``-DLAMMPS_MEMALIGN``, if you want to have memory Do not set ``-DLAMMPS_MEMALIGN``, if you want to have memory
allocated with the "malloc()" function call allocated with the ``malloc()`` function call
instead. ``-DLAMMPS_MEMALIGN`` **cannot** be used on Windows, as instead. ``-DLAMMPS_MEMALIGN`` **cannot** be used on Windows, as
Windows different function calls with different semantics for Windows different function calls with different semantics for
allocating aligned memory, that are not compatible with how LAMMPS allocating aligned memory, that are not compatible with how LAMMPS

9
doc/src/Commands_all.rst
View File

@ -1,4 +1,3 @@
.. only:: html .. only:: html
.. table_from_list:: .. table_from_list::
@ -15,12 +14,14 @@
* :doc:`KSpace styles <Commands_kspace>` * :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>` * :doc:`Dump styles <Commands_dump>`
.. raw:: latex
\clearpage
General commands General commands
================ ================
An alphabetic list of general LAMMPS commands. Note that style An alphabetic list of general LAMMPS commands.
commands with many variants, can be more easily accessed via the small
table above.
.. table_from_list:: .. table_from_list::
:columns: 6 :columns: 6

17
doc/src/Commands_bond.rst
View File

@ -1,4 +1,3 @@
.. only:: html .. only:: html
.. table_from_list:: .. table_from_list::
@ -17,8 +16,8 @@
.. _bond: .. _bond:
Bond_style potentials Bond styles
===================== ===========
All LAMMPS :doc:`bond_style <bond_style>` commands. Some styles have All LAMMPS :doc:`bond_style <bond_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in accelerated versions. This is indicated by additional letters in
@ -65,8 +64,8 @@ OPT.
.. _angle: .. _angle:
Angle_style potentials Angle styles
====================== ============
All LAMMPS :doc:`angle_style <angle_style>` commands. Some styles have All LAMMPS :doc:`angle_style <angle_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in accelerated versions. This is indicated by additional letters in
@ -113,8 +112,8 @@ OPT.
.. _dihedral: .. _dihedral:
Dihedral_style potentials Dihedral styles
========================= ===============
All LAMMPS :doc:`dihedral_style <dihedral_style>` commands. Some styles All LAMMPS :doc:`dihedral_style <dihedral_style>` commands. Some styles
have accelerated versions. This is indicated by additional letters in have accelerated versions. This is indicated by additional letters in
@ -153,8 +152,8 @@ OPT.
.. _improper: .. _improper:
Improper_style potentials Improper styles
========================= ===============
All LAMMPS :doc:`improper_style <improper_style>` commands. Some styles All LAMMPS :doc:`improper_style <improper_style>` commands. Some styles
have accelerated versions. This is indicated by additional letters in have accelerated versions. This is indicated by additional letters in

40
doc/src/Commands_category.rst
View File

@ -1,3 +1,7 @@
.. raw:: latex
\clearpage
Commands by category Commands by category
==================== ====================
@ -6,8 +10,8 @@ This page lists most of the LAMMPS commands, grouped by category. The
alphabetically. Style options for entries like fix, compute, pair etc. alphabetically. Style options for entries like fix, compute, pair etc.
have their own pages where they are listed alphabetically. have their own pages where they are listed alphabetically.
Initialization: Initialization
------------------------------ --------------
.. table_from_list:: .. table_from_list::
:columns: 5 :columns: 5
@ -18,8 +22,8 @@ Initialization:
* :doc:`suffix <suffix>` * :doc:`suffix <suffix>`
* :doc:`units <units>` * :doc:`units <units>`
Setup simulation box: Setup simulation box
------------------------------ --------------------
.. table_from_list:: .. table_from_list::
:columns: 4 :columns: 4
@ -31,8 +35,8 @@ Setup simulation box:
* :doc:`lattice <lattice>` * :doc:`lattice <lattice>`
* :doc:`region <region>` * :doc:`region <region>`
Setup atoms: Setup atoms
------------------------------ -----------
.. table_from_list:: .. table_from_list::
:columns: 4 :columns: 4
@ -55,8 +59,8 @@ Setup atoms:
* :doc:`set <set>` * :doc:`set <set>`
* :doc:`velocity <velocity>` * :doc:`velocity <velocity>`
Force fields: Force fields
------------------------------ ------------
.. table_from_list:: .. table_from_list::
:columns: 4 :columns: 4
@ -79,8 +83,8 @@ Force fields:
* :doc:`pair_write <pair_write>` * :doc:`pair_write <pair_write>`
* :doc:`special_bonds <special_bonds>` * :doc:`special_bonds <special_bonds>`
Settings: Settings
------------------------------ --------
.. table_from_list:: .. table_from_list::
:columns: 4 :columns: 4
@ -98,8 +102,8 @@ Settings:
* :doc:`timer <timer>` * :doc:`timer <timer>`
* :doc:`timestep <timestep>` * :doc:`timestep <timestep>`
Operations within timestepping (fixes) and diagnostics (computes): Operations within timestepping (fixes) and diagnostics (computes)
------------------------------------------------------------------------------------------ -----------------------------------------------------------------
.. table_from_list:: .. table_from_list::
:columns: 4 :columns: 4
@ -111,8 +115,8 @@ Operations within timestepping (fixes) and diagnostics (computes):
* :doc:`uncompute <uncompute>` * :doc:`uncompute <uncompute>`
* :doc:`unfix <unfix>` * :doc:`unfix <unfix>`
Output: Output
------------------------------ ------
.. table_from_list:: .. table_from_list::
:columns: 4 :columns: 4
@ -131,8 +135,8 @@ Output:
* :doc:`write_dump <write_dump>` * :doc:`write_dump <write_dump>`
* :doc:`write_restart <write_restart>` * :doc:`write_restart <write_restart>`
Actions: Actions
------------------------------ -------
.. table_from_list:: .. table_from_list::
:columns: 6 :columns: 6
@ -146,8 +150,8 @@ Actions:
* :doc:`tad <tad>` * :doc:`tad <tad>`
* :doc:`temper <temper>` * :doc:`temper <temper>`
Input script control: Input script control
------------------------------ --------------------
.. table_from_list:: .. table_from_list::
:columns: 7 :columns: 7

5
doc/src/Commands_compute.rst
View File

@ -1,4 +1,3 @@
.. only:: html .. only:: html
.. table_from_list:: .. table_from_list::
@ -15,8 +14,8 @@
* :doc:`KSpace styles <Commands_kspace>` * :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>` * :doc:`Dump styles <Commands_dump>`
Compute commands Compute styles
================ ==============
An alphabetic list of all LAMMPS :doc:`compute <compute>` commands. An alphabetic list of all LAMMPS :doc:`compute <compute>` commands.
Some styles have accelerated versions. This is indicated by Some styles have accelerated versions. This is indicated by

5
doc/src/Commands_dump.rst
View File

@ -1,4 +1,3 @@
.. only:: html .. only:: html
.. table_from_list:: .. table_from_list::
@ -15,8 +14,8 @@
* :doc:`KSpace styles <Commands_kspace>` * :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>` * :doc:`Dump styles <Commands_dump>`
Dump commands Dump styles
============= ===========
An alphabetic list of all LAMMPS :doc:`dump <dump>` commands. An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.

5
doc/src/Commands_fix.rst
View File

@ -1,4 +1,3 @@
.. only:: html .. only:: html
.. table_from_list:: .. table_from_list::
@ -15,8 +14,8 @@
* :doc:`KSpace styles <Commands_kspace>` * :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>` * :doc:`Dump styles <Commands_dump>`
Fix commands Fix styles
============ ==========
An alphabetic list of all LAMMPS :doc:`fix <fix>` commands. Some styles An alphabetic list of all LAMMPS :doc:`fix <fix>` commands. Some styles
have accelerated versions. This is indicated by additional letters in have accelerated versions. This is indicated by additional letters in

16
doc/src/Commands_input.rst
View File

@ -10,14 +10,14 @@ for any commands that may be processed later. Commands may set an
internal variable, read in a file, or run a simulation. These actions internal variable, read in a file, or run a simulation. These actions
can be grouped into three categories: can be grouped into three categories:
a) commands that change a global setting (examples: timestep, newton, a) commands that change a global setting (examples: :doc:`timestep <timestep>`, :doc:`newton <newton>`,
echo, log, thermo, restart), :doc:`echo <echo>`, :doc:`log <log>`, :doc:`thermo <thermo>`, :doc:`restart <restart>`),
b) commands that add, modify, remove, or replace "styles" that are b) commands that add, modify, remove, or replace "styles" that are
executed during a "run" (examples: pair_style, fix, compute, dump, executed during a "run" (examples: :doc:`pair_style <pair_style>`, :doc:`fix <fix>`, :doc:`compute <compute>`, :doc:`dump <dump>`,
thermo_style, pair_modify), and :doc:`thermo_style <thermo_style>`, :doc:`pair_modify <pair_modify>`), and
c) commands that execute a "run" or perform some other computation or c) commands that execute a "run" or perform some other computation or
operation (examples: print, run, minimize, temper, write_dump, rerun, operation (examples: :doc:`print <print>`, :doc:`run <run>`, :doc:`minimize <minimize>`, :doc:`temper <temper>`, :doc:`write_dump <write_dump>`, :doc:`rerun <rerun>`,
read_data, read_restart) :doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`)
Commands in category a) have default settings, which means you only Commands in category a) have default settings, which means you only
need to use the command if you wish to change the defaults. need to use the command if you wish to change the defaults.
@ -61,7 +61,7 @@ between commands in the c) category. The following rules apply:
<read_data>` command initializes the system by setting up the <read_data>` command initializes the system by setting up the
simulation box and assigning atoms to processors. If default values simulation box and assigning atoms to processors. If default values
are not desired, the :doc:`processors <processors>` and are not desired, the :doc:`processors <processors>` and
:doc:`boundary <boundary>` commands need to be used before read_data :doc:`boundary <boundary>` commands need to be used before ``read_data``
to tell LAMMPS how to map processors to the simulation box. to tell LAMMPS how to map processors to the simulation box.
Many input script errors are detected by LAMMPS and an ERROR or Many input script errors are detected by LAMMPS and an ERROR or
@ -70,6 +70,6 @@ more information on what errors mean. The documentation for each
command lists restrictions on how the command can be used. command lists restrictions on how the command can be used.
You can use the :ref:`-skiprun <skiprun>` command line flag You can use the :ref:`-skiprun <skiprun>` command line flag
to have LAMMPS skip the execution of any "run", "minimize", or similar to have LAMMPS skip the execution of any ``run``, ``minimize``, or similar
commands to check the entire input for correct syntax to avoid crashes commands to check the entire input for correct syntax to avoid crashes
on typos or syntax errors in long runs. on typos or syntax errors in long runs.

5
doc/src/Commands_kspace.rst
View File

@ -1,4 +1,3 @@
.. only:: html .. only:: html
.. table_from_list:: .. table_from_list::
@ -15,8 +14,8 @@
* :doc:`KSpace styles <Commands_kspace>` * :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>` * :doc:`Dump styles <Commands_dump>`
KSpace solvers KSpace styles
============== =============
All LAMMPS :doc:`kspace_style <kspace_style>` solvers. Some styles have All LAMMPS :doc:`kspace_style <kspace_style>` solvers. Some styles have
accelerated versions. This is indicated by additional letters in accelerated versions. This is indicated by additional letters in

9
doc/src/Commands_pair.rst
View File

@ -1,4 +1,3 @@
.. only:: html .. only:: html
.. table_from_list:: .. table_from_list::
@ -15,8 +14,8 @@
* :doc:`KSpace styles <Commands_kspace>` * :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>` * :doc:`Dump styles <Commands_dump>`
Pair_style potentials Pair styles
====================== ===========
All LAMMPS :doc:`pair_style <pair_style>` commands. Some styles have All LAMMPS :doc:`pair_style <pair_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in accelerated versions. This is indicated by additional letters in
@ -38,10 +37,6 @@ OPT.
* *
* *
* *
*
*
*
*
* :doc:`adp (ko) <pair_adp>` * :doc:`adp (ko) <pair_adp>`
* :doc:`agni (o) <pair_agni>` * :doc:`agni (o) <pair_agni>`
* :doc:`aip/water/2dm (t) <pair_aip_water_2dm>` * :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`

12
doc/src/Commands_parse.rst
View File

@ -42,8 +42,8 @@ LAMMPS:
If the $ is followed by text in curly brackets '{}', then the If the $ is followed by text in curly brackets '{}', then the
variable name is the text inside the curly brackets. If no curly variable name is the text inside the curly brackets. If no curly
brackets follow the $, then the variable name is the single character brackets follow the $, then the variable name is the single character
immediately following the $. Thus ${myTemp} and $x refer to variables immediately following the $. Thus ``${myTemp}`` and ``$x`` refer to variables
named "myTemp" and "x", while "$xx" will be interpreted as a variable named "myTemp" and "x", while ``$xx`` will be interpreted as a variable
named "x" followed by an "x" character. named "x" followed by an "x" character.
How the variable is converted to a text string depends on what style How the variable is converted to a text string depends on what style
@ -79,10 +79,10 @@ LAMMPS:
Additionally, the entire "immediate" variable expression may be Additionally, the entire "immediate" variable expression may be
followed by a colon, followed by a C-style format string, followed by a colon, followed by a C-style format string,
e.g. ":%f" or ":%.10g". The format string must be appropriate for e.g. ``:%f`` or ``:%.10g``. The format string must be appropriate for
a double-precision floating-point value. The format string is used a double-precision floating-point value. The format string is used
to output the result of the variable expression evaluation. If a to output the result of the variable expression evaluation. If a
format string is not specified, a high-precision "%.20g" is used as format string is not specified, a high-precision ``%.20g`` is used as
the default format. the default format.
This can be useful for formatting print output to a desired precision: This can be useful for formatting print output to a desired precision:
@ -101,8 +101,8 @@ LAMMPS:
variable b2 equal 4 variable b2 equal 4
print "B2 = ${b$a}" print "B2 = ${b$a}"
Nor can you specify an expression like "$($x-1.0)" for an immediate Nor can you specify an expression like ``$($x-1.0)`` for an immediate
variable, but you could use $(v_x-1.0), since the latter is valid variable, but you could use ``$(v_x-1.0)``, since the latter is valid
syntax for an :doc:`equal-style variable <variable>`. syntax for an :doc:`equal-style variable <variable>`.
See the :doc:`variable <variable>` command for more details of how See the :doc:`variable <variable>` command for more details of how

2
doc/src/Howto_bioFF.rst
View File

@ -73,7 +73,7 @@ with additional switching or shifting functions that ramp the energy
and/or force smoothly to zero between an inner :math:`(a)` and outer and/or force smoothly to zero between an inner :math:`(a)` and outer
:math:`(b)` cutoff. The older styles with *charmm* (not *charmmfsw* or :math:`(b)` cutoff. The older styles with *charmm* (not *charmmfsw* or
*charmmfsh*\ ) in their name compute the LJ and Coulombic interactions *charmmfsh*\ ) in their name compute the LJ and Coulombic interactions
with an energy switching function (esw) S(r) which ramps the energy with an energy switching function (esw) :math:`S(r)` which ramps the energy
smoothly to zero between the inner and outer cutoff. This can cause smoothly to zero between the inner and outer cutoff. This can cause
irregularities in pairwise forces (due to the discontinuous second irregularities in pairwise forces (due to the discontinuous second
derivative of energy at the boundaries of the switching region), which derivative of energy at the boundaries of the switching region), which

2
doc/src/Howto_couple.rst
View File

@ -36,7 +36,7 @@ the context of your application.
steps, invoke the command, etc. steps, invoke the command, etc.
In this scenario, the other code can be called as a library, as in In this scenario, the other code can be called as a library, as in
1., or it could be a stand-alone code, invoked by a system() call 1., or it could be a stand-alone code, invoked by a ``system()`` call
made by the command (assuming your parallel machine allows one or made by the command (assuming your parallel machine allows one or
more processors to start up another program). In the latter case the more processors to start up another program). In the latter case the
stand-alone code could communicate with LAMMPS through files that the stand-alone code could communicate with LAMMPS through files that the

8
doc/src/Howto_diffusion.rst
View File

@ -1,8 +1,8 @@
Calculate diffusion coefficients Calculate diffusion coefficients
================================ ================================
The diffusion coefficient D of a material can be measured in at least The diffusion coefficient :math:`D` of a material can be measured in at least
2 ways using various options in LAMMPS. See the examples/DIFFUSE 2 ways using various options in LAMMPS. See the ``examples/DIFFUSE``
directory for scripts that implement the 2 methods discussed here for directory for scripts that implement the 2 methods discussed here for
a simple Lennard-Jones fluid model. a simple Lennard-Jones fluid model.
@ -12,7 +12,7 @@ of the MSD versus time is proportional to the diffusion coefficient.
The instantaneous MSD values can be accumulated in a vector via the The instantaneous MSD values can be accumulated in a vector via the
:doc:`fix vector <fix_vector>` command, and a line fit to the vector to :doc:`fix vector <fix_vector>` command, and a line fit to the vector to
compute its slope via the :doc:`variable slope <variable>` function, and compute its slope via the :doc:`variable slope <variable>` function, and
thus extract D. thus extract :math:`D`.
The second method is to measure the velocity auto-correlation function The second method is to measure the velocity auto-correlation function
(VACF) of the system, via the :doc:`compute vacf <compute_vacf>` (VACF) of the system, via the :doc:`compute vacf <compute_vacf>`
@ -20,4 +20,4 @@ command. The time-integral of the VACF is proportional to the
diffusion coefficient. The instantaneous VACF values can be diffusion coefficient. The instantaneous VACF values can be
accumulated in a vector via the :doc:`fix vector <fix_vector>` command, accumulated in a vector via the :doc:`fix vector <fix_vector>` command,
and time integrated via the :doc:`variable trap <variable>` function, and time integrated via the :doc:`variable trap <variable>` function,
and thus extract D. and thus extract :math:`D`.

30
doc/src/Howto_elastic.rst
View File

@ -4,21 +4,27 @@ Calculate elastic constants
Elastic constants characterize the stiffness of a material. The formal Elastic constants characterize the stiffness of a material. The formal
definition is provided by the linear relation that holds between the definition is provided by the linear relation that holds between the
stress and strain tensors in the limit of infinitesimal deformation. stress and strain tensors in the limit of infinitesimal deformation.
In tensor notation, this is expressed as s_ij = C_ijkl \* e_kl, where In tensor notation, this is expressed as
the repeated indices imply summation. s_ij are the elements of the
symmetric stress tensor. e_kl are the elements of the symmetric strain .. math::
tensor. C_ijkl are the elements of the fourth rank tensor of elastic
constants. In three dimensions, this tensor has 3\^4=81 elements. Using s_{ij} = C_{ijkl} e_{kl}
Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij
is now the derivative of s_i w.r.t. e_j. Because s_i is itself a where
derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at the repeated indices imply summation. :math:`s_{ij}` are the elements of the
most 7\*6/2 = 21 distinct elements. symmetric stress tensor. :math:`e_{kl}` are the elements of the symmetric strain
tensor. :math:`C_{ijkl}` are the elements of the fourth rank tensor of elastic
constants. In three dimensions, this tensor has :math:`3^4=81` elements. Using
Voigt notation, the tensor can be written as a 6x6 matrix, where :math:`C_{ij}`
is now the derivative of :math:`s_i` w.r.t. :math:`e_j`. Because :math:`s_i` is itself a
derivative w.r.t. :math:`e_i`, it follows that :math:`C_{ij}` is also symmetric, with at
most :math:`\frac{7 \times 6}{2}` = 21 distinct elements.
At zero temperature, it is easy to estimate these derivatives by At zero temperature, it is easy to estimate these derivatives by
deforming the simulation box in one of the six directions using the deforming the simulation box in one of the six directions using the
:doc:`change_box <change_box>` command and measuring the change in the :doc:`change_box <change_box>` command and measuring the change in the
stress tensor. A general-purpose script that does this is given in the stress tensor. A general-purpose script that does this is given in the
examples/ELASTIC directory described on the :doc:`Examples <Examples>` ``examples/ELASTIC`` directory described on the :doc:`Examples <Examples>`
doc page. doc page.
Calculating elastic constants at finite temperature is more Calculating elastic constants at finite temperature is more
@ -33,7 +39,7 @@ the :doc:`compute born/matrix <compute_born_matrix>` command,
which works for any bonded or non-bonded potential in LAMMPS. which works for any bonded or non-bonded potential in LAMMPS.
The most expensive part of the calculation is the sampling of The most expensive part of the calculation is the sampling of
the stress fluctuations. Several examples of this method are the stress fluctuations. Several examples of this method are
provided in the examples/ELASTIC_T/BORN_MATRIX directory provided in the ``examples/ELASTIC_T/BORN_MATRIX`` directory
described on the :doc:`Examples <Examples>` doc page. described on the :doc:`Examples <Examples>` doc page.
A second way is to measure A second way is to measure
@ -43,7 +49,7 @@ the systematic and statistical errors in this method, the magnitude of
the deformation must be chosen judiciously, and care must be taken to the deformation must be chosen judiciously, and care must be taken to
fully equilibrate the deformed cell before sampling the stress fully equilibrate the deformed cell before sampling the stress
tensor. An example of this method is provided in the tensor. An example of this method is provided in the
examples/ELASTIC_T/DEFORMATION directory ``examples/ELASTIC_T/DEFORMATION`` directory
described on the :doc:`Examples <Examples>` doc page. described on the :doc:`Examples <Examples>` doc page.
Another approach is to sample the triclinic cell fluctuations Another approach is to sample the triclinic cell fluctuations

16
doc/src/Howto_kappa.rst
View File

@ -1,20 +1,22 @@
Calculate thermal conductivity Calculate thermal conductivity
============================== ==============================
The thermal conductivity kappa of a material can be measured in at The thermal conductivity :math:`\kappa` of a material can be measured in at
least 4 ways using various options in LAMMPS. See the examples/KAPPA least 4 ways using various options in LAMMPS. See the ``examples/KAPPA``
directory for scripts that implement the 4 methods discussed here for directory for scripts that implement the 4 methods discussed here for
a simple Lennard-Jones fluid model. Also, see the :doc:`Howto viscosity <Howto_viscosity>` page for an analogous discussion a simple Lennard-Jones fluid model. Also, see the :doc:`Howto viscosity <Howto_viscosity>` page for an analogous discussion
for viscosity. for viscosity.
The thermal conductivity tensor kappa is a measure of the propensity The thermal conductivity tensor :math:`\mathbf{\kappa}` is a measure of the propensity
of a material to transmit heat energy in a diffusive manner as given of a material to transmit heat energy in a diffusive manner as given
by Fourier's law by Fourier's law
J = -kappa grad(T) .. math::
where J is the heat flux in units of energy per area per time and J = -\kappa \cdot \text{grad}(T)
grad(T) is the spatial gradient of temperature. The thermal
where :math:`J` is the heat flux in units of energy per area per time and
:math:`\text{grad}(T)` is the spatial gradient of temperature. The thermal
conductivity thus has units of energy per distance per time per degree conductivity thus has units of energy per distance per time per degree
K and is often approximated as an isotropic quantity, i.e. as a K and is often approximated as an isotropic quantity, i.e. as a
scalar. scalar.
@ -49,7 +51,7 @@ details.
The fourth method is based on the Green-Kubo (GK) formula which The fourth method is based on the Green-Kubo (GK) formula which
relates the ensemble average of the auto-correlation of the heat flux relates the ensemble average of the auto-correlation of the heat flux
to kappa. The heat flux can be calculated from the fluctuations of to :math:`\kappa`. The heat flux can be calculated from the fluctuations of
per-atom potential and kinetic energies and per-atom stress tensor in per-atom potential and kinetic energies and per-atom stress tensor in
a steady-state equilibrated simulation. This is in contrast to the a steady-state equilibrated simulation. This is in contrast to the
two preceding non-equilibrium methods, where energy flows continuously two preceding non-equilibrium methods, where energy flows continuously

10
doc/src/Howto_multiple.rst
View File

@ -44,7 +44,7 @@ For large numbers of independent simulations, you can use
:doc:`variables <variable>` and the :doc:`next <next>` and :doc:`variables <variable>` and the :doc:`next <next>` and
:doc:`jump <jump>` commands to loop over the same input script :doc:`jump <jump>` commands to loop over the same input script
multiple times with different settings. For example, this multiple times with different settings. For example, this
script, named in.polymer script, named ``in.polymer``
.. code-block:: LAMMPS .. code-block:: LAMMPS
@ -57,7 +57,7 @@ script, named in.polymer
next d next d
jump in.polymer jump in.polymer
would run 8 simulations in different directories, using a data.polymer would run 8 simulations in different directories, using a ``data.polymer``
file in each directory. The same concept could be used to run the file in each directory. The same concept could be used to run the
same system at 8 different temperatures, using a temperature variable same system at 8 different temperatures, using a temperature variable
and storing the output in different log and dump files, for example and storing the output in different log and dump files, for example
@ -83,10 +83,10 @@ partition of processors. LAMMPS can be run on multiple partitions via
the :doc:`-partition command-line switch <Run_options>`. the :doc:`-partition command-line switch <Run_options>`.
In the last 2 examples, if LAMMPS were run on 3 partitions, the same In the last 2 examples, if LAMMPS were run on 3 partitions, the same
scripts could be used if the "index" and "loop" variables were scripts could be used if the ``index`` and ``loop`` variables were
replaced with *universe*\ -style variables, as described in the replaced with *universe*\ -style variables, as described in the
:doc:`variable <variable>` command. Also, the "next t" and "next a" :doc:`variable <variable>` command. Also, the :lammps:`next t` and :lammps:`next a`
commands would need to be replaced with a single "next a t" command. commands would need to be replaced with a single :lammps:`next a t` command.
With these modifications, the 8 simulations of each script would run With these modifications, the 8 simulations of each script would run
on the 3 partitions one after the other until all were finished. on the 3 partitions one after the other until all were finished.
Initially, 3 simulations would be started simultaneously, one on each Initially, 3 simulations would be started simultaneously, one on each

18
doc/src/Howto_restart.rst
View File

@ -26,8 +26,8 @@ scripts are based on. If that script had the line
restart 50 tmp.restart restart 50 tmp.restart
added to it, it would produce 2 binary restart files (tmp.restart.50 added to it, it would produce two binary restart files (``tmp.restart.50``
and tmp.restart.100) as it ran. and ``tmp.restart.100``) as it ran.
This script could be used to read the first restart file and re-run the This script could be used to read the first restart file and re-run the
last 50 timesteps: last 50 timesteps:
@ -47,21 +47,21 @@ last 50 timesteps:
run 50 run 50
Note that the following commands do not need to be repeated because Note that the following commands do not need to be repeated because
their settings are included in the restart file: *units, atom_style, their settings are included in the restart file: :lammps:`units`, :lammps:`atom_style`,
special_bonds, pair_style, bond_style*. However, these commands do :lammps:`special_bonds`, :lammps:`pair_style`, :lammps:`bond_style`. However, these commands do
need to be used, since their settings are not in the restart file: need to be used, since their settings are not in the restart file:
*neighbor, fix, timestep*\ . :lammps:`neighbor`, :lammps:`fix`, :lammps:`timestep`.
If you actually use this script to perform a restarted run, you will If you actually use this script to perform a restarted run, you will
notice that the thermodynamic data match at step 50 (if you also put a notice that the thermodynamic data match at step 50 (if you also put a
"thermo 50" command in the original script), but do not match at step :lammps:`thermo 50` command in the original script), but do not match at step
100. This is because the :doc:`fix langevin <fix_langevin>` command 100. This is because the :doc:`fix langevin <fix_langevin>` command
uses random numbers in a way that does not allow for perfect restarts. uses random numbers in a way that does not allow for perfect restarts.
As an alternate approach, the restart file could be converted to a data As an alternate approach, the restart file could be converted to a data
file as follows: file as follows:
.. code-block:: LAMMPS .. code-block:: bash
lmp_g++ -r tmp.restart.50 tmp.restart.data lmp_g++ -r tmp.restart.50 tmp.restart.data
@ -89,8 +89,8 @@ Then, this script could be used to re-run the last 50 steps:
reset_timestep 50 reset_timestep 50
run 50 run 50
Note that nearly all the settings specified in the original *in.chain* Note that nearly all the settings specified in the original ``in.chain``
script must be repeated, except the *pair_coeff* and *bond_coeff* script must be repeated, except the :lammps:`pair_coeff` and :lammps:`bond_coeff`
commands, since the new data file lists the force field coefficients. commands, since the new data file lists the force field coefficients.
Also, the :doc:`reset_timestep <reset_timestep>` command is used to tell Also, the :doc:`reset_timestep <reset_timestep>` command is used to tell
LAMMPS the current timestep. This value is stored in restart files, but LAMMPS the current timestep. This value is stored in restart files, but

10
doc/src/Howto_structured_data.rst
View File

@ -341,7 +341,12 @@ data files and obtain a list of dictionaries.
.. code-block:: .. code-block::
[{'timestep': 0, 'pe': -6.773368053259247, 'ke': 4.498875000000003}, {'timestep': 50, 'pe': -4.80824944183232, 'ke': 2.5257981827119798}, {'timestep': 100, 'pe': -4.787560887558151, 'ke': 2.5062598821985103}, {'timestep': 150, 'pe': -4.747103368600548, 'ke': 2.46609592554545}, {'timestep': 200, 'pe': -4.750905285854413, 'ke': 2.4701136792591694}, {'timestep': 250, 'pe': -4.777432735632181, 'ke': 2.4962152903997175}] [{'timestep': 0, 'pe': -6.773368053259247, 'ke': 4.498875000000003},
{'timestep': 50, 'pe': -4.80824944183232, 'ke': 2.5257981827119798},
{'timestep': 100, 'pe': -4.787560887558151, 'ke': 2.5062598821985103},
{'timestep': 150, 'pe': -4.747103368600548, 'ke': 2.46609592554545},
{'timestep': 200, 'pe': -4.750905285854413, 'ke': 2.4701136792591694},
{'timestep': 250, 'pe': -4.777432735632181, 'ke': 2.4962152903997175}]
Line Delimited JSON (LD-JSON) Line Delimited JSON (LD-JSON)
----------------------------- -----------------------------
@ -352,7 +357,8 @@ Each line represents one JSON object.
.. code-block:: LAMMPS .. code-block:: LAMMPS
fix extra all print 50 """{"timestep": $(step), "pe": $(pe), "ke": $(ke)}""" title "" file output.json screen no fix extra all print 50 """{"timestep": $(step), "pe": $(pe), "ke": $(ke)}""" &
title "" file output.json screen no
.. code-block:: json .. code-block:: json
:caption: output.json :caption: output.json

24
doc/src/Howto_viscosity.rst
View File

@ -1,22 +1,24 @@
Calculate viscosity Calculate viscosity
=================== ===================
The shear viscosity eta of a fluid can be measured in at least 6 ways The shear viscosity :math:`\eta` of a fluid can be measured in at least 6 ways
using various options in LAMMPS. See the examples/VISCOSITY directory using various options in LAMMPS. See the ``examples/VISCOSITY`` directory
for scripts that implement the 5 methods discussed here for a simple for scripts that implement the 5 methods discussed here for a simple
Lennard-Jones fluid model and 1 method for SPC/E water model. Lennard-Jones fluid model and 1 method for SPC/E water model.
Also, see the :doc:`page on calculating thermal conductivity <Howto_kappa>` Also, see the :doc:`page on calculating thermal conductivity <Howto_kappa>`
for an analogous discussion for thermal conductivity. for an analogous discussion for thermal conductivity.
Eta is a measure of the propensity of a fluid to transmit momentum in :math:`\eta` is a measure of the propensity of a fluid to transmit momentum in
a direction perpendicular to the direction of velocity or momentum a direction perpendicular to the direction of velocity or momentum
flow. Alternatively it is the resistance the fluid has to being flow. Alternatively it is the resistance the fluid has to being
sheared. It is given by sheared. It is given by
J = -eta grad(Vstream) .. math::
where J is the momentum flux in units of momentum per area per time. J = -\eta \cdot \text{grad}(V_{\text{stream}})
and grad(Vstream) is the spatial gradient of the velocity of the fluid
where :math:`J` is the momentum flux in units of momentum per area per time.
and :math:`\text{grad}(V_{\text{stream}})` is the spatial gradient of the velocity of the fluid
moving in another direction, normal to the area through which the moving in another direction, normal to the area through which the
momentum flows. Viscosity thus has units of pressure-time. momentum flows. Viscosity thus has units of pressure-time.
@ -38,11 +40,11 @@ velocity to prevent the fluid from heating up.
In both cases, the velocity profile setup in the fluid by this In both cases, the velocity profile setup in the fluid by this
procedure can be monitored by the :doc:`fix ave/chunk <fix_ave_chunk>` procedure can be monitored by the :doc:`fix ave/chunk <fix_ave_chunk>`
command, which determines grad(Vstream) in the equation above. command, which determines :math:`\text{grad}(V_{\text{stream}})` in the equation above.
E.g. the derivative in the y-direction of the Vx component of fluid E.g. the derivative in the y-direction of the :math:`V_x` component of fluid
motion or grad(Vstream) = dVx/dy. The Pxy off-diagonal component of motion or :math:`\text{grad}(V_{\text{stream}}) = \frac{\text{d} V_x}{\text{d} y}`. The :math:`P_{xy}` off-diagonal component of
the pressure or stress tensor, as calculated by the :doc:`compute pressure <compute_pressure>` command, can also be monitored, which the pressure or stress tensor, as calculated by the :doc:`compute pressure <compute_pressure>` command, can also be monitored, which
is the J term in the equation above. See the :doc:`Howto nemd <Howto_nemd>` page for details on NEMD simulations. is the :math:`J` term in the equation above. See the :doc:`Howto nemd <Howto_nemd>` page for details on NEMD simulations.
The third method is to perform a reverse non-equilibrium MD simulation The third method is to perform a reverse non-equilibrium MD simulation
using the :doc:`fix viscosity <fix_viscosity>` command which implements using the :doc:`fix viscosity <fix_viscosity>` command which implements
@ -55,7 +57,7 @@ See the :doc:`fix viscosity <fix_viscosity>` command for details.
The fourth method is based on the Green-Kubo (GK) formula which The fourth method is based on the Green-Kubo (GK) formula which
relates the ensemble average of the auto-correlation of the relates the ensemble average of the auto-correlation of the
stress/pressure tensor to eta. This can be done in a fully stress/pressure tensor to :math:`\eta`. This can be done in a fully
equilibrated simulation which is in contrast to the two preceding equilibrated simulation which is in contrast to the two preceding
non-equilibrium methods, where momentum flows continuously through the non-equilibrium methods, where momentum flows continuously through the
simulation box. simulation box.

2
doc/src/Howto_viz.rst
View File

@ -6,7 +6,7 @@ analyzed in a variety of ways.
LAMMPS snapshots are created by the :doc:`dump <dump>` command, which LAMMPS snapshots are created by the :doc:`dump <dump>` command, which
can create files in several formats. The native LAMMPS dump format is a can create files in several formats. The native LAMMPS dump format is a
text file (see "dump atom" or "dump custom") which can be visualized by text file (see :lammps:`dump atom` or :lammps:`dump custom`) which can be visualized by
`several visualization tools <https://www.lammps.org/viz.html>`_ for MD `several visualization tools <https://www.lammps.org/viz.html>`_ for MD
simulation trajectories. `OVITO <https://www.ovito.org>`_ and `VMD simulation trajectories. `OVITO <https://www.ovito.org>`_ and `VMD
<https://www.ks.uiuc.edu/Research/vmd>`_ seem to be the most popular <https://www.ks.uiuc.edu/Research/vmd>`_ seem to be the most popular

58
doc/src/Install.rst
View File

@ -35,35 +35,35 @@ you **must** build LAMMPS from the source code.
These are the files and subdirectories in the LAMMPS distribution: These are the files and subdirectories in the LAMMPS distribution:
+------------+---------------------------------------------+ +-----------------+---------------------------------------------+
| README | Short description of the LAMMPS package | | ``README`` | Short description of the LAMMPS package |
+------------+---------------------------------------------+ +-----------------+---------------------------------------------+
| LICENSE | GNU General Public License (GPL) | | ``LICENSE`` | GNU General Public License (GPL) |
+------------+---------------------------------------------+ +-----------------+---------------------------------------------+
| SECURITY.md| Security policy for the LAMMPS package | | ``SECURITY.md`` | Security policy for the LAMMPS package |
+------------+---------------------------------------------+ +-----------------+---------------------------------------------+
| bench | benchmark inputs | | ``bench`` | benchmark inputs |
+------------+---------------------------------------------+ +-----------------+---------------------------------------------+
| cmake | CMake build files | | ``cmake`` | CMake build files |
+------------+---------------------------------------------+ +-----------------+---------------------------------------------+
| doc | documentation and tools to build the manual | | ``doc`` | documentation and tools to build the manual |
+------------+---------------------------------------------+ +-----------------+---------------------------------------------+
| examples | example input files | | ``examples`` | example input files |
+------------+---------------------------------------------+ +-----------------+---------------------------------------------+
| fortran | Fortran module for LAMMPS library interface | | ``fortran`` | Fortran module for LAMMPS library interface |
+------------+---------------------------------------------+ +-----------------+---------------------------------------------+
| lib | additional provided or external libraries | | ``lib`` | additional provided or external libraries |
+------------+---------------------------------------------+ +-----------------+---------------------------------------------+
| potentials | selected interatomic potential files | | ``potentials`` | selected interatomic potential files |
+------------+---------------------------------------------+ +-----------------+---------------------------------------------+
| python | Python module for LAMMPS library interface | | ``python`` | Python module for LAMMPS library interface |
+------------+---------------------------------------------+ +-----------------+---------------------------------------------+
| src | LAMMPS source files | | ``src`` | LAMMPS source files |
+------------+---------------------------------------------+ +-----------------+---------------------------------------------+
| tools | pre- and post-processing tools | | ``tools`` | pre- and post-processing tools |
+------------+---------------------------------------------+ +-----------------+---------------------------------------------+
| unittest | source code and inputs for testing LAMMPS | | ``unittest`` | source code and inputs for testing LAMMPS |
+------------+---------------------------------------------+ +-----------------+---------------------------------------------+
You will have all of these if you downloaded the LAMMPS source code. You will have all of these if you downloaded the LAMMPS source code.
You will have only some of them if you downloaded executables, as You will have only some of them if you downloaded executables, as

4
doc/src/Install_git.rst
View File

@ -60,7 +60,7 @@ between them at any time using "git checkout <branch name>".)
files (mostly by accident). If you do not need access to the entire files (mostly by accident). If you do not need access to the entire
commit history (most people don't), you can speed up the "cloning" commit history (most people don't), you can speed up the "cloning"
process and reduce local disk space requirements by using the process and reduce local disk space requirements by using the
*--depth* git command line flag. That will create a "shallow clone" ``--depth`` git command line flag. That will create a "shallow clone"
of the repository, which contains only a subset of the git history. of the repository, which contains only a subset of the git history.
Using a depth of 1000 is usually sufficient to include the head Using a depth of 1000 is usually sufficient to include the head
commits of the *develop*, the *release*, and the *maintenance* commits of the *develop*, the *release*, and the *maintenance*
@ -122,7 +122,7 @@ changed. How to do this depends on the build system you are using.
.. code-block:: bash .. code-block:: bash
cmake . --build cmake --build .
CMake should auto-detect whether it needs to re-run the CMake CMake should auto-detect whether it needs to re-run the CMake
configuration step and otherwise redo the build for all files configuration step and otherwise redo the build for all files

2
doc/src/Install_tarball.rst
View File

@ -31,7 +31,7 @@ command:
tar -xzvf lammps*.tar.gz tar -xzvf lammps*.tar.gz
This will create a LAMMPS directory with the version date in its name, This will create a LAMMPS directory with the version date in its name,
e.g. lammps-28Mar23. e.g. ``lammps-28Mar23``.
---------- ----------

2
doc/src/Install_windows.rst
View File

@ -34,7 +34,7 @@ When you download the installer package, you run it on your Windows
machine. It will then prompt you with a dialog, where you can choose machine. It will then prompt you with a dialog, where you can choose
the installation directory, unpack and copy several executables, the installation directory, unpack and copy several executables,
potential files, documentation PDFs, selected example files, etc. It potential files, documentation PDFs, selected example files, etc. It
will then update a few system settings (e.g. PATH, LAMMPS_POTENTIALS) will then update a few system settings (e.g. ``PATH``, ``LAMMPS_POTENTIALS``)
and add an entry into the Start Menu (with references to the and add an entry into the Start Menu (with references to the
documentation, LAMMPS homepage and more). From that menu, there is documentation, LAMMPS homepage and more). From that menu, there is
also a link to an uninstaller that removes the files and undoes the also a link to an uninstaller that removes the files and undoes the

522
doc/src/Packages_details.rst
View File

File diff suppressed because it is too large Load Diff

98
doc/src/Packages_list.rst
View File

@ -10,8 +10,8 @@ the rest of LAMMPS.
The "Examples" column is a subdirectory in the examples directory of the The "Examples" column is a subdirectory in the examples directory of the
distribution which has one or more input scripts that use the package. distribution which has one or more input scripts that use the package.
E.g. "peptide" refers to the examples/peptide directory; PACKAGES/atc refers E.g. ``peptide`` refers to the ``examples/peptide`` directory; ``PACKAGES/atc`` refers
to the examples/PACKAGES/atc directory. The "Lib" column indicates to the ``examples/PACKAGES/atc`` directory. The "Lib" column indicates``
whether an extra library is needed to build and use the package: whether an extra library is needed to build and use the package:
* no = no library * no = no library
@ -21,7 +21,7 @@ whether an extra library is needed to build and use the package:
.. list-table:: .. list-table::
:header-rows: 1 :header-rows: 1
:widths: auto :widths: 20 20 30 25 5
* - Package * - Package
- Description - Description
@ -31,7 +31,7 @@ whether an extra library is needed to build and use the package:
* - :ref:`ADIOS <PKG-ADIOS>` * - :ref:`ADIOS <PKG-ADIOS>`
- dump output via ADIOS - dump output via ADIOS
- :doc:`dump adios <dump_adios>` - :doc:`dump adios <dump_adios>`
- PACKAGES/adios - ``PACKAGES/adios``
- ext - ext
* - :ref:`AMOEBA <PKG-AMOEBA>` * - :ref:`AMOEBA <PKG-AMOEBA>`
- AMOEBA and HIPPO force fields - AMOEBA and HIPPO force fields
@ -46,17 +46,17 @@ whether an extra library is needed to build and use the package:
* - :ref:`ATC <PKG-ATC>` * - :ref:`ATC <PKG-ATC>`
- Atom-to-Continuum coupling - Atom-to-Continuum coupling
- :doc:`fix atc <fix_atc>` - :doc:`fix atc <fix_atc>`
- PACKAGES/atc - ``PACKAGES/atc``
- int - int
* - :ref:`AWPMD <PKG-AWPMD>` * - :ref:`AWPMD <PKG-AWPMD>`
- wave packet MD - wave packet MD
- :doc:`pair_style awpmd/cut <pair_awpmd>` - :doc:`pair_style awpmd/cut <pair_awpmd>`
- PACKAGES/awpmd - ``PACKAGES/awpmd``
- int - int
* - :ref:`BOCS <PKG-BOCS>` * - :ref:`BOCS <PKG-BOCS>`
- BOCS bottom up coarse graining - BOCS bottom up coarse graining
- :doc:`fix bocs <fix_bocs>` - :doc:`fix bocs <fix_bocs>`
- PACKAGES/bocs - ``PACKAGES/bocs``
- no - no
* - :ref:`BODY <PKG-BODY>` * - :ref:`BODY <PKG-BODY>`
- body-style particles - body-style particles
@ -71,17 +71,17 @@ whether an extra library is needed to build and use the package:
* - :ref:`BROWNIAN <PKG-BROWNIAN>` * - :ref:`BROWNIAN <PKG-BROWNIAN>`
- Brownian dynamics, self-propelled particles - Brownian dynamics, self-propelled particles
- :doc:`fix brownian <fix_brownian>`, :doc:`fix propel/self <fix_propel_self>` - :doc:`fix brownian <fix_brownian>`, :doc:`fix propel/self <fix_propel_self>`
- PACKAGES/brownian - ``PACKAGES/brownian``
- no - no
* - :ref:`CG-DNA <PKG-CG-DNA>` * - :ref:`CG-DNA <PKG-CG-DNA>`
- coarse-grained DNA force fields - coarse-grained DNA force fields
- src/CG-DNA/README - ``src/CG-DNA/README``
- PACKAGES/cgdna - ``PACKAGES/cgdna``
- no - no
* - :ref:`CG-SPICA <PKG-CG-SPICA>` * - :ref:`CG-SPICA <PKG-CG-SPICA>`
- SPICA (SDK) coarse-graining model - SPICA (SDK) coarse-graining model
- :doc:`pair_style lj/spica <pair_spica>` - :doc:`pair_style lj/spica <pair_spica>`
- PACKAGES/cgspica - ``PACKAGES/cgspica``
- no - no
* - :ref:`CLASS2 <PKG-CLASS2>` * - :ref:`CLASS2 <PKG-CLASS2>`
- class 2 force fields - class 2 force fields
@ -96,7 +96,7 @@ whether an extra library is needed to build and use the package:
* - :ref:`COLVARS <PKG-COLVARS>` * - :ref:`COLVARS <PKG-COLVARS>`
- `Colvars collective variables library <https://colvars.github.io/>`_ - `Colvars collective variables library <https://colvars.github.io/>`_
- :doc:`fix colvars <fix_colvars>` - :doc:`fix colvars <fix_colvars>`
- PACKAGES/colvars - ``PACKAGES/colvars``
- int - int
* - :ref:`COMPRESS <PKG-COMPRESS>` * - :ref:`COMPRESS <PKG-COMPRESS>`
- I/O compression - I/O compression
@ -111,12 +111,12 @@ whether an extra library is needed to build and use the package:
* - :ref:`DIELECTRIC <PKG-DIELECTRIC>` * - :ref:`DIELECTRIC <PKG-DIELECTRIC>`
- dielectric boundary solvers and force styles - dielectric boundary solvers and force styles
- :doc:`compute efield/atom <compute_efield_atom>` - :doc:`compute efield/atom <compute_efield_atom>`
- PACKAGES/dielectric - ``PACKAGES/dielectric``
- no - no
* - :ref:`DIFFRACTION <PKG-DIFFRACTION>` * - :ref:`DIFFRACTION <PKG-DIFFRACTION>`
- virtual x-ray and electron diffraction - virtual x-ray and electron diffraction
- :doc:`compute xrd <compute_xrd>` - :doc:`compute xrd <compute_xrd>`
- PACKAGES/diffraction - ``PACKAGES/diffraction``
- no - no
* - :ref:`DIPOLE <PKG-DIPOLE>` * - :ref:`DIPOLE <PKG-DIPOLE>`
- point dipole particles - point dipole particles
@ -126,37 +126,37 @@ whether an extra library is needed to build and use the package:
* - :ref:`DPD-BASIC <PKG-DPD-BASIC>` * - :ref:`DPD-BASIC <PKG-DPD-BASIC>`
- basic DPD models - basic DPD models
- :doc:`pair_styles dpd <pair_dpd>` :doc:`dpd/ext <pair_dpd_ext>` - :doc:`pair_styles dpd <pair_dpd>` :doc:`dpd/ext <pair_dpd_ext>`
- PACKAGES/dpd-basic - ``PACKAGES/dpd-basic``
- no - no
* - :ref:`DPD-MESO <PKG-DPD-MESO>` * - :ref:`DPD-MESO <PKG-DPD-MESO>`
- mesoscale DPD models - mesoscale DPD models
- :doc:`pair_style edpd <pair_mesodpd>` - :doc:`pair_style edpd <pair_mesodpd>`
- PACKAGES/dpd-meso - ``PACKAGES/dpd-meso``
- no - no
* - :ref:`DPD-REACT <PKG-DPD-REACT>` * - :ref:`DPD-REACT <PKG-DPD-REACT>`
- reactive dissipative particle dynamics - reactive dissipative particle dynamics
- src/DPD-REACT/README - ``src/DPD-REACT/README``
- PACKAGES/dpd-react - ``PACKAGES/dpd-react``
- no - no
* - :ref:`DPD-SMOOTH <PKG-DPD-SMOOTH>` * - :ref:`DPD-SMOOTH <PKG-DPD-SMOOTH>`
- smoothed dissipative particle dynamics - smoothed dissipative particle dynamics
- src/DPD-SMOOTH/README - ``src/DPD-SMOOTH/README``
- PACKAGES/dpd-smooth - ``PACKAGES/dpd-smooth``
- no - no
* - :ref:`DRUDE <PKG-DRUDE>` * - :ref:`DRUDE <PKG-DRUDE>`
- Drude oscillators - Drude oscillators
- :doc:`Howto drude <Howto_drude>` - :doc:`Howto drude <Howto_drude>`
- PACKAGES/drude - ``PACKAGES/drude``
- no - no
* - :ref:`EFF <PKG-EFF>` * - :ref:`EFF <PKG-EFF>`
- electron force field - electron force field
- :doc:`pair_style eff/cut <pair_eff>` - :doc:`pair_style eff/cut <pair_eff>`
- PACKAGES/eff - ``PACKAGES/eff``
- no - no
* - :ref:`ELECTRODE <PKG-ELECTRODE>` * - :ref:`ELECTRODE <PKG-ELECTRODE>`
- electrode charges to match potential - electrode charges to match potential
- :doc:`fix electrode/conp <fix_electrode>` - :doc:`fix electrode/conp <fix_electrode>`
- PACKAGES/electrode - ``PACKAGES/electrode``
- no - no
* - :ref:`EXTRA-COMMAND <PKG-EXTRA-COMMAND>` * - :ref:`EXTRA-COMMAND <PKG-EXTRA-COMMAND>`
- additional command styles - additional command styles
@ -191,7 +191,7 @@ whether an extra library is needed to build and use the package:
* - :ref:`FEP <PKG-FEP>` * - :ref:`FEP <PKG-FEP>`
- free energy perturbation - free energy perturbation
- :doc:`compute fep <compute_fep>` - :doc:`compute fep <compute_fep>`
- PACKAGES/fep - ``PACKAGES/fep``
- no - no
* - :ref:`GPU <PKG-GPU>` * - :ref:`GPU <PKG-GPU>`
- GPU-enabled styles - GPU-enabled styles
@ -216,7 +216,7 @@ whether an extra library is needed to build and use the package:
* - :ref:`INTERLAYER <PKG-INTERLAYER>` * - :ref:`INTERLAYER <PKG-INTERLAYER>`
- Inter-layer pair potentials - Inter-layer pair potentials
- :doc:`several pair styles <Commands_pair>` - :doc:`several pair styles <Commands_pair>`
- PACKAGES/interlayer - ``PACKAGES/interlayer``
- no - no
* - :ref:`KIM <PKG-KIM>` * - :ref:`KIM <PKG-KIM>`
- OpenKIM wrapper - OpenKIM wrapper
@ -236,22 +236,22 @@ whether an extra library is needed to build and use the package:
* - :ref:`LATBOLTZ <PKG-LATBOLTZ>` * - :ref:`LATBOLTZ <PKG-LATBOLTZ>`
- Lattice Boltzmann fluid - Lattice Boltzmann fluid
- :doc:`fix lb/fluid <fix_lb_fluid>` - :doc:`fix lb/fluid <fix_lb_fluid>`
- PACKAGES/latboltz - ``PACKAGES/latboltz``
- no - no
* - :ref:`LEPTON <PKG-LEPTON>` * - :ref:`LEPTON <PKG-LEPTON>`
- evaluate strings as potential function - evaluate strings as potential function
- :doc:`pair_style lepton <pair_lepton>` - :doc:`pair_style lepton <pair_lepton>`
- PACKAGES/lepton - ``PACKAGES/lepton``
- int - int
* - :ref:`MACHDYN <PKG-MACHDYN>` * - :ref:`MACHDYN <PKG-MACHDYN>`
- smoothed Mach dynamics - smoothed Mach dynamics
- `SMD User Guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ - `SMD User Guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_
- PACKAGES/machdyn - ``PACKAGES/machdyn``
- ext - ext
* - :ref:`MANIFOLD <PKG-MANIFOLD>` * - :ref:`MANIFOLD <PKG-MANIFOLD>`
- motion on 2d surfaces - motion on 2d surfaces
- :doc:`fix manifoldforce <fix_manifoldforce>` - :doc:`fix manifoldforce <fix_manifoldforce>`
- PACKAGES/manifold - ``PACKAGES/manifold``
- no - no
* - :ref:`MANYBODY <PKG-MANYBODY>` * - :ref:`MANYBODY <PKG-MANYBODY>`
- many-body potentials - many-body potentials
@ -266,7 +266,7 @@ whether an extra library is needed to build and use the package:
* - :ref:`MDI <PKG-MDI>` * - :ref:`MDI <PKG-MDI>`
- client-server code coupling - client-server code coupling
- :doc:`MDI Howto <Howto_mdi>` - :doc:`MDI Howto <Howto_mdi>`
- PACKAGES/mdi - ``PACKAGES/mdi``
- ext - ext
* - :ref:`MEAM <PKG-MEAM>` * - :ref:`MEAM <PKG-MEAM>`
- modified EAM potential (C++) - modified EAM potential (C++)
@ -276,12 +276,12 @@ whether an extra library is needed to build and use the package:
* - :ref:`MESONT <PKG-MESONT>` * - :ref:`MESONT <PKG-MESONT>`
- mesoscopic tubular potential model - mesoscopic tubular potential model
- pair styles :doc:`mesocnt <pair_mesocnt>` - pair styles :doc:`mesocnt <pair_mesocnt>`
- PACKAGES/mesont - ``PACKAGES/mesont``
- no - no
* - :ref:`MGPT <PKG-MGPT>` * - :ref:`MGPT <PKG-MGPT>`
- fast MGPT multi-ion potentials - fast MGPT multi-ion potentials
- :doc:`pair_style mgpt <pair_mgpt>` - :doc:`pair_style mgpt <pair_mgpt>`
- PACKAGES/mgpt - ``PACKAGES/mgpt``
- no - no
* - :ref:`MISC <PKG-MISC>` * - :ref:`MISC <PKG-MISC>`
- miscellaneous single-file commands - miscellaneous single-file commands
@ -291,7 +291,7 @@ whether an extra library is needed to build and use the package:
* - :ref:`ML-HDNNP <PKG-ML-HDNNP>` * - :ref:`ML-HDNNP <PKG-ML-HDNNP>`
- High-dimensional neural network potentials - High-dimensional neural network potentials
- :doc:`pair_style hdnnp <pair_hdnnp>` - :doc:`pair_style hdnnp <pair_hdnnp>`
- PACKAGES/hdnnp - ``PACKAGES/hdnnp``
- ext - ext
* - :ref:`ML-IAP <PKG-ML-IAP>` * - :ref:`ML-IAP <PKG-ML-IAP>`
- multiple machine learning potentials - multiple machine learning potentials
@ -301,7 +301,7 @@ whether an extra library is needed to build and use the package:
* - :ref:`ML-PACE <PKG-ML-PACE>` * - :ref:`ML-PACE <PKG-ML-PACE>`
- Atomic Cluster Expansion potential - Atomic Cluster Expansion potential
- :doc:`pair pace <pair_pace>` - :doc:`pair pace <pair_pace>`
- PACKAGES/pace - ``PACKAGES/pace``
- ext - ext
* - :ref:`ML-POD <PKG-ML-POD>` * - :ref:`ML-POD <PKG-ML-POD>`
- Proper orthogonal decomposition potentials - Proper orthogonal decomposition potentials
@ -311,12 +311,12 @@ whether an extra library is needed to build and use the package:
* - :ref:`ML-QUIP <PKG-ML-QUIP>` * - :ref:`ML-QUIP <PKG-ML-QUIP>`
- QUIP/libatoms interface - QUIP/libatoms interface
- :doc:`pair_style quip <pair_quip>` - :doc:`pair_style quip <pair_quip>`
- PACKAGES/quip - ``PACKAGES/quip``
- ext - ext
* - :ref:`ML-RANN <PKG-ML-RANN>` * - :ref:`ML-RANN <PKG-ML-RANN>`
- Pair style for RANN potentials - Pair style for RANN potentials
- :doc:`pair rann <pair_rann>` - :doc:`pair rann <pair_rann>`
- PACKAGES/rann - ``PACKAGES/rann``
- no - no
* - :ref:`ML-SNAP <PKG-ML-SNAP>` * - :ref:`ML-SNAP <PKG-ML-SNAP>`
- quantum-fitted potential - quantum-fitted potential
@ -326,12 +326,12 @@ whether an extra library is needed to build and use the package:
* - :ref:`ML-UF3 <PKG-ML-UF3>` * - :ref:`ML-UF3 <PKG-ML-UF3>`
- quantum-fitted ultra fast potentials - quantum-fitted ultra fast potentials
- :doc:`pair_style uf3 <pair_uf3>` - :doc:`pair_style uf3 <pair_uf3>`
- PACKAGES/uf3 - ``PACKAGES/uf3``
- no - no
* - :ref:`MOFFF <PKG-MOFFF>` * - :ref:`MOFFF <PKG-MOFFF>`
- styles for `MOF-FF <MOFplus_>`_ force field - styles for `MOF-FF <MOFplus_>`_ force field
- :doc:`pair_style buck6d/coul/gauss <pair_buck6d_coul_gauss>` - :doc:`pair_style buck6d/coul/gauss <pair_buck6d_coul_gauss>`
- PACKAGES/mofff - ``PACKAGES/mofff``
- no - no
* - :ref:`MOLECULE <PKG-MOLECULE>` * - :ref:`MOLECULE <PKG-MOLECULE>`
- molecular system force fields - molecular system force fields
@ -361,7 +361,7 @@ whether an extra library is needed to build and use the package:
* - :ref:`ORIENT <PKG-ORIENT>` * - :ref:`ORIENT <PKG-ORIENT>`
- fixes for orientation depended forces - fixes for orientation depended forces
- :doc:`fix orient/* <fix_orient>` - :doc:`fix orient/* <fix_orient>`
- PACKAGES/orient_eco - ``PACKAGES/orient_eco``
- no - no
* - :ref:`PERI <PKG-PERI>` * - :ref:`PERI <PKG-PERI>`
- Peridynamics models - Peridynamics models
@ -371,7 +371,7 @@ whether an extra library is needed to build and use the package:
* - :ref:`PHONON <PKG-PHONON>` * - :ref:`PHONON <PKG-PHONON>`
- phonon dynamical matrix - phonon dynamical matrix
- :doc:`fix phonon <fix_phonon>` - :doc:`fix phonon <fix_phonon>`
- PACKAGES/phonon - ``PACKAGES/phonon``
- no - no
* - :ref:`PLUGIN <PKG-PLUGIN>` * - :ref:`PLUGIN <PKG-PLUGIN>`
- Plugin loader command - Plugin loader command
@ -381,7 +381,7 @@ whether an extra library is needed to build and use the package:
* - :ref:`PLUMED <PKG-PLUMED>` * - :ref:`PLUMED <PKG-PLUMED>`
- `PLUMED free energy library <https://www.plumed.org>`_ - `PLUMED free energy library <https://www.plumed.org>`_
- :doc:`fix plumed <fix_plumed>` - :doc:`fix plumed <fix_plumed>`
- PACKAGES/plumed - ``PACKAGES/plumed``
- ext - ext
* - :ref:`POEMS <PKG-POEMS>` * - :ref:`POEMS <PKG-POEMS>`
- coupled rigid body motion - coupled rigid body motion
@ -406,7 +406,7 @@ whether an extra library is needed to build and use the package:
* - :ref:`QMMM <PKG-QMMM>` * - :ref:`QMMM <PKG-QMMM>`
- QM/MM coupling - QM/MM coupling
- :doc:`fix qmmm <fix_qmmm>` - :doc:`fix qmmm <fix_qmmm>`
- PACKAGES/qmmm - ``PACKAGES/qmmm``
- ext - ext
* - :ref:`QTB <PKG-QTB>` * - :ref:`QTB <PKG-QTB>`
- quantum nuclear effects - quantum nuclear effects
@ -421,7 +421,7 @@ whether an extra library is needed to build and use the package:
* - :ref:`REACTION <PKG-REACTION>` * - :ref:`REACTION <PKG-REACTION>`
- chemical reactions in classical MD - chemical reactions in classical MD
- :doc:`fix bond/react <fix_bond_react>` - :doc:`fix bond/react <fix_bond_react>`
- PACKAGES/reaction - ``PACKAGES/reaction``
- no - no
* - :ref:`REAXFF <PKG-REAXFF>` * - :ref:`REAXFF <PKG-REAXFF>`
- ReaxFF potential (C/C++) - ReaxFF potential (C/C++)
@ -441,7 +441,7 @@ whether an extra library is needed to build and use the package:
* - :ref:`SCAFACOS <PKG-SCAFACOS>` * - :ref:`SCAFACOS <PKG-SCAFACOS>`
- wrapper for ScaFaCoS Kspace solver - wrapper for ScaFaCoS Kspace solver
- :doc:`kspace_style scafacos <kspace_style>` - :doc:`kspace_style scafacos <kspace_style>`
- PACKAGES/scafacos - ``PACKAGES/scafacos``
- ext - ext
* - :ref:`SHOCK <PKG-SHOCK>` * - :ref:`SHOCK <PKG-SHOCK>`
- shock loading methods - shock loading methods
@ -451,12 +451,12 @@ whether an extra library is needed to build and use the package:
* - :ref:`SMTBQ <PKG-SMTBQ>` * - :ref:`SMTBQ <PKG-SMTBQ>`
- second moment tight binding potentials - second moment tight binding potentials
- pair styles :doc:`smtbq <pair_smtbq>`, :doc:`smatb <pair_smatb>` - pair styles :doc:`smtbq <pair_smtbq>`, :doc:`smatb <pair_smatb>`
- PACKAGES/smtbq - ``PACKAGES/smtbq``
- no - no
* - :ref:`SPH <PKG-SPH>` * - :ref:`SPH <PKG-SPH>`
- smoothed particle hydrodynamics - smoothed particle hydrodynamics
- `SPH User Guide <PDF/SPH_LAMMPS_userguide.pdf>`_ - `SPH User Guide <PDF/SPH_LAMMPS_userguide.pdf>`_
- PACKAGES/sph - ``PACKAGES/sph``
- no - no
* - :ref:`SPIN <PKG-SPIN>` * - :ref:`SPIN <PKG-SPIN>`
- magnetic atomic spin dynamics - magnetic atomic spin dynamics
@ -471,12 +471,12 @@ whether an extra library is needed to build and use the package:
* - :ref:`TALLY <PKG-TALLY>` * - :ref:`TALLY <PKG-TALLY>`
- pairwise tally computes - pairwise tally computes
- :doc:`compute XXX/tally <compute_tally>` - :doc:`compute XXX/tally <compute_tally>`
- PACKAGES/tally - ``PACKAGES/tally``
- no - no
* - :ref:`UEF <PKG-UEF>` * - :ref:`UEF <PKG-UEF>`
- extensional flow - extensional flow
- :doc:`fix nvt/uef <fix_nh_uef>` - :doc:`fix nvt/uef <fix_nh_uef>`
- PACKAGES/uef - ``PACKAGES/uef``
- no - no
* - :ref:`VORONOI <PKG-VORONOI>` * - :ref:`VORONOI <PKG-VORONOI>`
- Voronoi tesselation - Voronoi tesselation
@ -491,7 +491,7 @@ whether an extra library is needed to build and use the package:
* - :ref:`YAFF <PKG-YAFF>` * - :ref:`YAFF <PKG-YAFF>`
- additional styles implemented in YAFF - additional styles implemented in YAFF
- :doc:`angle_style cross <angle_cross>` - :doc:`angle_style cross <angle_cross>`
- PACKAGES/yaff - ``PACKAGES/yaff``
- no - no
.. _MOFplus: https://www.mofplus.org/content/show/MOF-FF .. _MOFplus: https://www.mofplus.org/content/show/MOF-FF

14
doc/src/Run_basics.rst
View File

@ -2,8 +2,8 @@ Basics of running LAMMPS
======================== ========================
LAMMPS is run from the command line, reading commands from a file via LAMMPS is run from the command line, reading commands from a file via
the -in command line flag, or from standard input. Using the "-in the ``-in`` command line flag, or from standard input. Using the ``-in
in.file" variant is recommended (see note below). The name of the in.file`` variant is recommended (see note below). The name of the
LAMMPS executable is either ``lmp`` or ``lmp_<machine>`` with LAMMPS executable is either ``lmp`` or ``lmp_<machine>`` with
`<machine>` being the machine string used when compiling LAMMPS. This `<machine>` being the machine string used when compiling LAMMPS. This
is required when compiling LAMMPS with the traditional build system is required when compiling LAMMPS with the traditional build system
@ -35,7 +35,7 @@ executable itself can be placed elsewhere.
form is required. form is required.
As LAMMPS runs it prints info to the screen and a logfile named As LAMMPS runs it prints info to the screen and a logfile named
*log.lammps*\ . More info about output is given on the :doc:`screen and ``log.lammps``. More info about output is given on the :doc:`screen and
logfile output <Run_output>` page. logfile output <Run_output>` page.
If LAMMPS encounters errors in the input script or while running a If LAMMPS encounters errors in the input script or while running a
@ -69,12 +69,12 @@ defaults are often adequate.
For example, it is often important to bind MPI tasks (processes) to For example, it is often important to bind MPI tasks (processes) to
physical cores (processor affinity), so that the operating system does physical cores (processor affinity), so that the operating system does
not migrate them during a simulation. If this is not the default not migrate them during a simulation. If this is not the default
behavior on your machine, the mpirun option "--bind-to core" (OpenMPI) behavior on your machine, the mpirun option ``--bind-to core`` (OpenMPI)
or "-bind-to core" (MPICH) can be used. or ``-bind-to core`` (MPICH) can be used.
If the LAMMPS command(s) you are using support multi-threading, you If the LAMMPS command(s) you are using support multi-threading, you
can set the number of threads per MPI task via the environment can set the number of threads per MPI task via the environment
variable OMP_NUM_THREADS, before you launch LAMMPS: variable ``OMP_NUM_THREADS``, before you launch LAMMPS:
.. code-block:: bash .. code-block:: bash
@ -91,7 +91,7 @@ packages and which commands support multi-threading.
You can experiment with running LAMMPS using any of the input scripts You can experiment with running LAMMPS using any of the input scripts
provided in the examples or bench directory. Input scripts are named provided in the examples or bench directory. Input scripts are named
in.\* and sample outputs are named log.\*.P where P is the number of ``in.*`` and sample outputs are named ``log.*.P`` where P is the number of
processors it was run on. processors it was run on.
Some of the examples or benchmarks require LAMMPS to be built with Some of the examples or benchmarks require LAMMPS to be built with

24
doc/src/Run_options.rst
View File

@ -275,13 +275,13 @@ impact can be significant, especially for large parallel runs.
Invoke the :doc:`package <package>` command with style and args. The Invoke the :doc:`package <package>` command with style and args. The
syntax is the same as if the command appeared at the top of the input syntax is the same as if the command appeared at the top of the input
script. For example "-package gpu 2" or "-pk gpu 2" is the same as script. For example ``-package gpu 2`` or ``-pk gpu 2`` is the same as
:doc:`package gpu 2 <package>` in the input script. The possible styles :doc:`package gpu 2 <package>` in the input script. The possible styles
and args are documented on the :doc:`package <package>` doc page. This and args are documented on the :doc:`package <package>` doc page. This
switch can be used multiple times, e.g. to set options for the switch can be used multiple times, e.g. to set options for the
INTEL and OPENMP packages which can be used together. INTEL and OPENMP packages which can be used together.
Along with the "-suffix" command-line switch, this is a convenient Along with the ``-suffix`` command-line switch, this is a convenient
mechanism for invoking accelerator packages and their options without mechanism for invoking accelerator packages and their options without
having to edit an input script. having to edit an input script.
@ -300,7 +300,7 @@ specify the number of processors in each partition. Arguments of the
form MxN mean M partitions, each with N processors. Arguments of the form MxN mean M partitions, each with N processors. Arguments of the
form N mean a single partition with N processors. The sum of form N mean a single partition with N processors. The sum of
processors in all partitions must equal P. Thus the command processors in all partitions must equal P. Thus the command
"-partition 8x2 4 5" has 10 partitions and runs on a total of 25 ``-partition 8x2 4 5`` has 10 partitions and runs on a total of 25
processors. processors.
Running with multiple partitions can be useful for running Running with multiple partitions can be useful for running
@ -378,8 +378,8 @@ processors will be in the first partition, the second set in the second
partition. The -reorder command-line switch can alter this so that partition. The -reorder command-line switch can alter this so that
the first N procs in the first partition and one proc in the second partition the first N procs in the first partition and one proc in the second partition
will be ordered consecutively, e.g. as the cores on one physical node. will be ordered consecutively, e.g. as the cores on one physical node.
This can boost performance. For example, if you use "-reorder nth 4" This can boost performance. For example, if you use ``-reorder nth 4``
and "-partition 9 3" and you are running on 12 processors, the and ``-partition 9 3`` and you are running on 12 processors, the
processors will be reordered from processors will be reordered from
.. parsed-literal:: .. parsed-literal::
@ -584,11 +584,11 @@ style that accepts arguments. It allows for two packages to be
specified. The first package specified is the default and will be used specified. The first package specified is the default and will be used
if it is available. If no style is available for the first package, if it is available. If no style is available for the first package,
the style for the second package will be used if available. For the style for the second package will be used if available. For
example, "-suffix hybrid intel omp" will use styles from the example, ``-suffix hybrid intel omp`` will use styles from the
INTEL package if they are installed and available, but styles for INTEL package if they are installed and available, but styles for
the OPENMP package otherwise. the OPENMP package otherwise.
Along with the "-package" command-line switch, this is a convenient Along with the ``-package`` command-line switch, this is a convenient
mechanism for invoking accelerator packages and their options without mechanism for invoking accelerator packages and their options without
having to edit an input script. having to edit an input script.
@ -605,30 +605,30 @@ variant version does not exist, the standard version is created.
For the GPU package, using this command-line switch also invokes the For the GPU package, using this command-line switch also invokes the
default GPU settings, as if the command "package gpu 1" were used at default GPU settings, as if the command "package gpu 1" were used at
the top of your input script. These settings can be changed by using the top of your input script. These settings can be changed by using
the "-package gpu" command-line switch or the :doc:`package gpu <package>` command in your script. the ``-package gpu`` command-line switch or the :doc:`package gpu <package>` command in your script.
For the INTEL package, using this command-line switch also For the INTEL package, using this command-line switch also
invokes the default INTEL settings, as if the command "package invokes the default INTEL settings, as if the command "package
intel 1" were used at the top of your input script. These settings intel 1" were used at the top of your input script. These settings
can be changed by using the "-package intel" command-line switch or can be changed by using the ``-package intel`` command-line switch or
the :doc:`package intel <package>` command in your script. If the the :doc:`package intel <package>` command in your script. If the
OPENMP package is also installed, the hybrid style with "intel omp" OPENMP package is also installed, the hybrid style with "intel omp"
arguments can be used to make the omp suffix a second choice, if a arguments can be used to make the omp suffix a second choice, if a
requested style is not available in the INTEL package. It will requested style is not available in the INTEL package. It will
also invoke the default OPENMP settings, as if the command "package also invoke the default OPENMP settings, as if the command "package
omp 0" were used at the top of your input script. These settings can omp 0" were used at the top of your input script. These settings can
be changed by using the "-package omp" command-line switch or the be changed by using the ``-package omp`` command-line switch or the
:doc:`package omp <package>` command in your script. :doc:`package omp <package>` command in your script.
For the KOKKOS package, using this command-line switch also invokes For the KOKKOS package, using this command-line switch also invokes
the default KOKKOS settings, as if the command "package kokkos" were the default KOKKOS settings, as if the command "package kokkos" were
used at the top of your input script. These settings can be changed used at the top of your input script. These settings can be changed
by using the "-package kokkos" command-line switch or the :doc:`package kokkos <package>` command in your script. by using the ``-package kokkos`` command-line switch or the :doc:`package kokkos <package>` command in your script.
For the OMP package, using this command-line switch also invokes the For the OMP package, using this command-line switch also invokes the
default OMP settings, as if the command "package omp 0" were used at default OMP settings, as if the command "package omp 0" were used at
the top of your input script. These settings can be changed by using the top of your input script. These settings can be changed by using
the "-package omp" command-line switch or the :doc:`package omp <package>` command in your script. the ``-package omp`` command-line switch or the :doc:`package omp <package>` command in your script.
The :doc:`suffix <suffix>` command can also be used within an input The :doc:`suffix <suffix>` command can also be used within an input
script to set a suffix, or to turn off or back on any suffix setting script to set a suffix, or to turn off or back on any suffix setting

16
doc/src/Speed_bench.rst
View File

@ -15,7 +15,7 @@ The 5 standard problems are as follow:
#. LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55 #. LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55
neighbors per atom), NVE integration neighbors per atom), NVE integration
#. Chain = bead-spring polymer melt of 100-mer chains, FENE bonds and LJ #. Chain = bead-spring polymer melt of 100-mer chains, FENE bonds and LJ
pairwise interactions with a 2\^(1/6) sigma cutoff (5 neighbors per pairwise interactions with a :math:`2^{\frac{1}{6}}` sigma cutoff (5 neighbors per
atom), NVE integration atom), NVE integration
#. EAM = metallic solid, Cu EAM potential with 4.95 Angstrom cutoff (45 #. EAM = metallic solid, Cu EAM potential with 4.95 Angstrom cutoff (45
neighbors per atom), NVE integration neighbors per atom), NVE integration
@ -29,19 +29,19 @@ The 5 standard problems are as follow:
Input files for these 5 problems are provided in the bench directory Input files for these 5 problems are provided in the bench directory
of the LAMMPS distribution. Each has 32,000 atoms and runs for 100 of the LAMMPS distribution. Each has 32,000 atoms and runs for 100
timesteps. The size of the problem (number of atoms) can be varied timesteps. The size of the problem (number of atoms) can be varied
using command-line switches as described in the bench/README file. using command-line switches as described in the ``bench/README`` file.
This is an easy way to test performance and either strong or weak This is an easy way to test performance and either strong or weak
scalability on your machine. scalability on your machine.
The bench directory includes a few log.\* files that show performance The bench directory includes a few ``log.*`` files that show performance
of these 5 problems on 1 or 4 cores of Linux desktop. The bench/FERMI of these 5 problems on 1 or 4 cores of Linux desktop. The ``bench/FERMI``
and bench/KEPLER directories have input files and scripts and instructions and ``bench/KEPLER`` directories have input files and scripts and instructions
for running the same (or similar) problems using OpenMP or GPU or Xeon for running the same (or similar) problems using OpenMP or GPU or Xeon
Phi acceleration options. See the README files in those directories and the Phi acceleration options. See the ``README`` files in those directories and the
:doc:`Accelerator packages <Speed_packages>` pages for instructions on how :doc:`Accelerator packages <Speed_packages>` pages for instructions on how
to build LAMMPS and run on that kind of hardware. to build LAMMPS and run on that kind of hardware.
The bench/POTENTIALS directory has input files which correspond to the The ``bench/POTENTIALS`` directory has input files which correspond to the
table of results on the table of results on the
`Potentials <https://www.lammps.org/bench.html#potentials>`_ section of `Potentials <https://www.lammps.org/bench.html#potentials>`_ section of
the Benchmarks web page. So you can also run those test problems on the Benchmarks web page. So you can also run those test problems on
@ -50,7 +50,7 @@ your machine.
The `billion-atom <https://www.lammps.org/bench.html#billion>`_ section The `billion-atom <https://www.lammps.org/bench.html#billion>`_ section
of the Benchmarks web page has performance data for very large of the Benchmarks web page has performance data for very large
benchmark runs of simple Lennard-Jones (LJ) models, which use the benchmark runs of simple Lennard-Jones (LJ) models, which use the
bench/in.lj input script. ``bench/in.lj`` input script.
---------- ----------

37
doc/src/Speed_gpu.rst
View File

@ -38,10 +38,10 @@ to have an NVIDIA GPU and install the corresponding NVIDIA CUDA
toolkit software on your system (this is only tested on Linux toolkit software on your system (this is only tested on Linux
and unsupported on Windows): and unsupported on Windows):
* Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/\*/information * Check if you have an NVIDIA GPU: ``cat /proc/driver/nvidia/gpus/\*/information``
* Go to https://developer.nvidia.com/cuda-downloads * Go to https://developer.nvidia.com/cuda-downloads
* Install a driver and toolkit appropriate for your system (SDK is not necessary) * Install a driver and toolkit appropriate for your system (SDK is not necessary)
* Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to * Run ``lammps/lib/gpu/nvc_get_devices`` (after building the GPU library, see below) to
list supported devices and properties list supported devices and properties
To compile and use this package in OpenCL mode, you currently need To compile and use this package in OpenCL mode, you currently need
@ -51,7 +51,7 @@ installed. There can be multiple of them for the same or different hardware
(GPUs, CPUs, Accelerators) installed at the same time. OpenCL refers to those (GPUs, CPUs, Accelerators) installed at the same time. OpenCL refers to those
as 'platforms'. The GPU library will try to auto-select the best suitable platform, as 'platforms'. The GPU library will try to auto-select the best suitable platform,
but this can be overridden using the platform option of the :doc:`package <package>` but this can be overridden using the platform option of the :doc:`package <package>`
command. run lammps/lib/gpu/ocl_get_devices to get a list of available command. run ``lammps/lib/gpu/ocl_get_devices`` to get a list of available
platforms and devices with a suitable ICD available. platforms and devices with a suitable ICD available.
To compile and use this package for Intel GPUs, OpenCL or the Intel oneAPI To compile and use this package for Intel GPUs, OpenCL or the Intel oneAPI
@ -63,7 +63,7 @@ provides optimized C++, MPI, and many other libraries and tools. See:
If you do not have a discrete GPU card installed, this package can still provide If you do not have a discrete GPU card installed, this package can still provide
significant speedups on some CPUs that include integrated GPUs. Additionally, for significant speedups on some CPUs that include integrated GPUs. Additionally, for
many macs, OpenCL is already included with the OS and Makefiles are available many macs, OpenCL is already included with the OS and Makefiles are available
in the lib/gpu directory. in the ``lib/gpu`` directory.
To compile and use this package in HIP mode, you have to have the AMD ROCm To compile and use this package in HIP mode, you have to have the AMD ROCm
software installed. Versions of ROCm older than 3.5 are currently deprecated software installed. Versions of ROCm older than 3.5 are currently deprecated
@ -94,31 +94,36 @@ shared by 4 MPI tasks.
The GPU package also has limited support for OpenMP for both The GPU package also has limited support for OpenMP for both
multi-threading and vectorization of routines that are run on the CPUs. multi-threading and vectorization of routines that are run on the CPUs.
This requires that the GPU library and LAMMPS are built with flags to This requires that the GPU library and LAMMPS are built with flags to
enable OpenMP support (e.g. -fopenmp). Some styles for time integration enable OpenMP support (e.g. ``-fopenmp``). Some styles for time integration
are also available in the GPU package. These run completely on the CPUs are also available in the GPU package. These run completely on the CPUs
in full double precision, but exploit multi-threading and vectorization in full double precision, but exploit multi-threading and vectorization
for faster performance. for faster performance.
Use the "-sf gpu" :doc:`command-line switch <Run_options>`, which will Use the ``-sf gpu`` :doc:`command-line switch <Run_options>`, which will
automatically append "gpu" to styles that support it. Use the "-pk automatically append "gpu" to styles that support it. Use the ``-pk
gpu Ng" :doc:`command-line switch <Run_options>` to set Ng = # of gpu Ng`` :doc:`command-line switch <Run_options>` to set ``Ng`` = # of
GPUs/node to use. If Ng is 0, the number is selected automatically as GPUs/node to use. If ``Ng`` is 0, the number is selected automatically as
the number of matching GPUs that have the highest number of compute the number of matching GPUs that have the highest number of compute
cores. cores.
.. code-block:: bash .. code-block:: bash
lmp_machine -sf gpu -pk gpu 1 -in in.script # 1 MPI task uses 1 GPU # 1 MPI task uses 1 GPU
mpirun -np 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node lmp_machine -sf gpu -pk gpu 1 -in in.script
mpirun -np 48 -ppn 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # ditto on 4 16-core nodes
Note that if the "-sf gpu" switch is used, it also issues a default # 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node
mpirun -np 12 lmp_machine -sf gpu -pk gpu 2 -in in.script
# ditto on 4 16-core nodes
mpirun -np 48 -ppn 12 lmp_machine -sf gpu -pk gpu 2 -in in.script
Note that if the ``-sf gpu`` switch is used, it also issues a default
:doc:`package gpu 0 <package>` command, which will result in :doc:`package gpu 0 <package>` command, which will result in
automatic selection of the number of GPUs to use. automatic selection of the number of GPUs to use.
Using the "-pk" switch explicitly allows for setting of the number of Using the ``-pk`` switch explicitly allows for setting of the number of
GPUs/node to use and additional options. Its syntax is the same as GPUs/node to use and additional options. Its syntax is the same as
the "package gpu" command. See the :doc:`package <package>` the ``package gpu`` command. See the :doc:`package <package>`
command page for details, including the default values used for command page for details, including the default values used for
all its options if it is not specified. all its options if it is not specified.
@ -141,7 +146,7 @@ Use the :doc:`suffix gpu <suffix>` command, or you can explicitly add an
pair_style lj/cut/gpu 2.5 pair_style lj/cut/gpu 2.5
You must also use the :doc:`package gpu <package>` command to enable the You must also use the :doc:`package gpu <package>` command to enable the
GPU package, unless the "-sf gpu" or "-pk gpu" :doc:`command-line switches <Run_options>` were used. It specifies the number of GPU package, unless the ``-sf gpu`` or ``-pk gpu`` :doc:`command-line switches <Run_options>` were used. It specifies the number of
GPUs/node to use, as well as other options. GPUs/node to use, as well as other options.
**Speed-ups to expect:** **Speed-ups to expect:**

125
doc/src/Speed_intel.rst
View File

@ -41,7 +41,7 @@ precision mode. Performance improvements are shown compared to
LAMMPS *without using other acceleration packages* as these are LAMMPS *without using other acceleration packages* as these are
under active development (and subject to performance changes). The under active development (and subject to performance changes). The
measurements were performed using the input files available in measurements were performed using the input files available in
the src/INTEL/TEST directory with the provided run script. the ``src/INTEL/TEST`` directory with the provided run script.
These are scalable in size; the results given are with 512K These are scalable in size; the results given are with 512K
particles (524K for Liquid Crystal). Most of the simulations are particles (524K for Liquid Crystal). Most of the simulations are
standard LAMMPS benchmarks (indicated by the filename extension in standard LAMMPS benchmarks (indicated by the filename extension in
@ -56,7 +56,7 @@ Results are speedups obtained on Intel Xeon E5-2697v4 processors
Knights Landing), and Intel Xeon Gold 6148 processors (code-named Knights Landing), and Intel Xeon Gold 6148 processors (code-named
Skylake) with "June 2017" LAMMPS built with Intel Parallel Studio Skylake) with "June 2017" LAMMPS built with Intel Parallel Studio
2017 update 2. Results are with 1 MPI task per physical core. See 2017 update 2. Results are with 1 MPI task per physical core. See
*src/INTEL/TEST/README* for the raw simulation rates and ``src/INTEL/TEST/README`` for the raw simulation rates and
instructions to reproduce. instructions to reproduce.
---------- ----------
@ -82,9 +82,9 @@ order of operations compared to LAMMPS without acceleration:
* The *newton* setting applies to all atoms, not just atoms shared * The *newton* setting applies to all atoms, not just atoms shared
between MPI tasks between MPI tasks
* Vectorization can change the order for adding pairwise forces * Vectorization can change the order for adding pairwise forces
* When using the -DLMP_USE_MKL_RNG define (all included intel optimized * When using the ``-DLMP_USE_MKL_RNG`` define (all included intel optimized
makefiles do) at build time, the random number generator for makefiles do) at build time, the random number generator for
dissipative particle dynamics (pair style dpd/intel) uses the Mersenne dissipative particle dynamics (``pair style dpd/intel``) uses the Mersenne
Twister generator included in the Intel MKL library (that should be Twister generator included in the Intel MKL library (that should be
more robust than the default Masaglia random number generator) more robust than the default Masaglia random number generator)
@ -106,36 +106,36 @@ LAMMPS should be built with the INTEL package installed.
Simulations should be run with 1 MPI task per physical *core*, Simulations should be run with 1 MPI task per physical *core*,
not *hardware thread*\ . not *hardware thread*\ .
* Edit src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi as necessary. * Edit ``src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi`` as necessary.
* Set the environment variable KMP_BLOCKTIME=0 * Set the environment variable ``KMP_BLOCKTIME=0``
* "-pk intel 0 omp $t -sf intel" added to LAMMPS command-line * ``-pk intel 0 omp $t -sf intel`` added to LAMMPS command-line
* $t should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi * ``$t`` should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi
* For some of the simple 2-body potentials without long-range * For some of the simple 2-body potentials without long-range
electrostatics, performance and scalability can be better with electrostatics, performance and scalability can be better with
the "newton off" setting added to the input script the ``newton off`` setting added to the input script
* For simulations on higher node counts, add "processors \* \* \* grid * For simulations on higher node counts, add ``processors * * * grid
numa" to the beginning of the input script for better scalability numa`` to the beginning of the input script for better scalability
* If using *kspace_style pppm* in the input script, add * If using ``kspace_style pppm`` in the input script, add
"kspace_modify diff ad" for better performance ``kspace_modify diff ad`` for better performance
For Intel Xeon Phi CPUs: For Intel Xeon Phi CPUs:
* Runs should be performed using MCDRAM. * Runs should be performed using MCDRAM.
For simulations using *kspace_style pppm* on Intel CPUs supporting For simulations using ``kspace_style pppm`` on Intel CPUs supporting
AVX-512: AVX-512:
* Add "kspace_modify diff ad" to the input script * Add ``kspace_modify diff ad`` to the input script
* The command-line option should be changed to * The command-line option should be changed to
"-pk intel 0 omp $r lrt yes -sf intel" where $r is the number of ``-pk intel 0 omp $r lrt yes -sf intel`` where ``$r`` is the number of
threads minus 1. threads minus 1.
* Do not use thread affinity (set KMP_AFFINITY=none) * Do not use thread affinity (set ``KMP_AFFINITY=none``)
* The "newton off" setting may provide better scalability * The ``newton off`` setting may provide better scalability
For Intel Xeon Phi co-processors (Offload): For Intel Xeon Phi co-processors (Offload):
* Edit src/MAKE/OPTIONS/Makefile.intel_co-processor as necessary * Edit ``src/MAKE/OPTIONS/Makefile.intel_co-processor`` as necessary
* "-pk intel N omp 1" added to command-line where N is the number of * ``-pk intel N omp 1`` added to command-line where ``N`` is the number of
co-processors per node. co-processors per node.
---------- ----------
@ -209,7 +209,7 @@ See the :ref:`Build extras <intel>` page for
instructions. Some additional details are covered here. instructions. Some additional details are covered here.
For building with make, several example Makefiles for building with For building with make, several example Makefiles for building with
the Intel compiler are included with LAMMPS in the src/MAKE/OPTIONS/ the Intel compiler are included with LAMMPS in the ``src/MAKE/OPTIONS/``
directory: directory:
.. code-block:: bash .. code-block:: bash
@ -239,35 +239,35 @@ However, if you do not have co-processors on your system, building
without offload support will produce a smaller binary. without offload support will produce a smaller binary.
The general requirements for Makefiles with the INTEL package The general requirements for Makefiles with the INTEL package
are as follows. When using Intel compilers, "-restrict" is required are as follows. When using Intel compilers, ``-restrict`` is required
and "-qopenmp" is highly recommended for CCFLAGS and LINKFLAGS. and ``-qopenmp`` is highly recommended for ``CCFLAGS`` and ``LINKFLAGS``.
CCFLAGS should include "-DLMP_INTEL_USELRT" (unless POSIX Threads ``CCFLAGS`` should include ``-DLMP_INTEL_USELRT`` (unless POSIX Threads
are not supported in the build environment) and "-DLMP_USE_MKL_RNG" are not supported in the build environment) and ``-DLMP_USE_MKL_RNG``
(unless Intel Math Kernel Library (MKL) is not available in the build (unless Intel Math Kernel Library (MKL) is not available in the build
environment). For Intel compilers, LIB should include "-ltbbmalloc" environment). For Intel compilers, ``LIB`` should include ``-ltbbmalloc``
or if the library is not available, "-DLMP_INTEL_NO_TBB" can be added or if the library is not available, ``-DLMP_INTEL_NO_TBB`` can be added
to CCFLAGS. For builds supporting offload, "-DLMP_INTEL_OFFLOAD" is to ``CCFLAGS``. For builds supporting offload, ``-DLMP_INTEL_OFFLOAD`` is
required for CCFLAGS and "-qoffload" is required for LINKFLAGS. Other required for ``CCFLAGS`` and ``-qoffload`` is required for ``LINKFLAGS``. Other
recommended CCFLAG options for best performance are "-O2 -fno-alias recommended ``CCFLAG`` options for best performance are ``-O2 -fno-alias
-ansi-alias -qoverride-limits fp-model fast=2 -no-prec-div". -ansi-alias -qoverride-limits fp-model fast=2 -no-prec-div``.
.. note:: .. note::
See the src/INTEL/README file for additional flags that See the ``src/INTEL/README`` file for additional flags that
might be needed for best performance on Intel server processors might be needed for best performance on Intel server processors
code-named "Skylake". code-named "Skylake".
.. note:: .. note::
The vectorization and math capabilities can differ depending on The vectorization and math capabilities can differ depending on
the CPU. For Intel compilers, the "-x" flag specifies the type of the CPU. For Intel compilers, the ``-x`` flag specifies the type of
processor for which to optimize. "-xHost" specifies that the compiler processor for which to optimize. ``-xHost`` specifies that the compiler
should build for the processor used for compiling. For Intel Xeon Phi should build for the processor used for compiling. For Intel Xeon Phi
x200 series processors, this option is "-xMIC-AVX512". For fourth x200 series processors, this option is ``-xMIC-AVX512``. For fourth
generation Intel Xeon (v4/Broadwell) processors, "-xCORE-AVX2" should generation Intel Xeon (v4/Broadwell) processors, ``-xCORE-AVX2`` should
be used. For older Intel Xeon processors, "-xAVX" will perform best be used. For older Intel Xeon processors, ``-xAVX`` will perform best
in general for the different simulations in LAMMPS. The default in general for the different simulations in LAMMPS. The default
in most of the example Makefiles is to use "-xHost", however this in most of the example Makefiles is to use ``-xHost``, however this
should not be used when cross-compiling. should not be used when cross-compiling.
Running LAMMPS with the INTEL package Running LAMMPS with the INTEL package
@ -304,11 +304,11 @@ almost all cases.
uniform. Unless disabled at build time, affinity for MPI tasks and uniform. Unless disabled at build time, affinity for MPI tasks and
OpenMP threads on the host (CPU) will be set by default on the host OpenMP threads on the host (CPU) will be set by default on the host
*when using offload to a co-processor*\ . In this case, it is unnecessary *when using offload to a co-processor*\ . In this case, it is unnecessary
to use other methods to control affinity (e.g. taskset, numactl, to use other methods to control affinity (e.g. ``taskset``, ``numactl``,
I_MPI_PIN_DOMAIN, etc.). This can be disabled with the *no_affinity* ``I_MPI_PIN_DOMAIN``, etc.). This can be disabled with the *no_affinity*
option to the :doc:`package intel <package>` command or by disabling the option to the :doc:`package intel <package>` command or by disabling the
option at build time (by adding -DINTEL_OFFLOAD_NOAFFINITY to the option at build time (by adding ``-DINTEL_OFFLOAD_NOAFFINITY`` to the
CCFLAGS line of your Makefile). Disabling this option is not ``CCFLAGS`` line of your Makefile). Disabling this option is not
recommended, especially when running on a machine with Intel recommended, especially when running on a machine with Intel
Hyper-Threading technology disabled. Hyper-Threading technology disabled.
@ -316,7 +316,7 @@ Run with the INTEL package from the command line
""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""""""""""""""""""""""""""""""""""""
To enable INTEL optimizations for all available styles used in To enable INTEL optimizations for all available styles used in
the input script, the "-sf intel" :doc:`command-line switch <Run_options>` can be used without any requirement for the input script, the ``-sf intel`` :doc:`command-line switch <Run_options>` can be used without any requirement for
editing the input script. This switch will automatically append editing the input script. This switch will automatically append
"intel" to styles that support it. It also invokes a default command: "intel" to styles that support it. It also invokes a default command:
:doc:`package intel 1 <package>`. This package command is used to set :doc:`package intel 1 <package>`. This package command is used to set
@ -329,15 +329,15 @@ will be used with automatic balancing of work between the CPU and the
co-processor. co-processor.
You can specify different options for the INTEL package by using You can specify different options for the INTEL package by using
the "-pk intel Nphi" :doc:`command-line switch <Run_options>` with the ``-pk intel Nphi`` :doc:`command-line switch <Run_options>` with
keyword/value pairs as specified in the documentation. Here, Nphi = # keyword/value pairs as specified in the documentation. Here, ``Nphi`` = #
of Xeon Phi co-processors/node (ignored without offload of Xeon Phi co-processors/node (ignored without offload
support). Common options to the INTEL package include *omp* to support). Common options to the INTEL package include *omp* to
override any OMP_NUM_THREADS setting and specify the number of OpenMP override any ``OMP_NUM_THREADS`` setting and specify the number of OpenMP
threads, *mode* to set the floating-point precision mode, and *lrt* to threads, *mode* to set the floating-point precision mode, and *lrt* to
enable Long-Range Thread mode as described below. See the :doc:`package intel <package>` command for details, including the default values enable Long-Range Thread mode as described below. See the :doc:`package intel <package>` command for details, including the default values
used for all its options if not specified, and how to set the number used for all its options if not specified, and how to set the number
of OpenMP threads via the OMP_NUM_THREADS environment variable if of OpenMP threads via the ``OMP_NUM_THREADS`` environment variable if
desired. desired.
Examples (see documentation for your MPI/Machine for differences in Examples (see documentation for your MPI/Machine for differences in
@ -345,8 +345,13 @@ launching MPI applications):
.. code-block:: bash .. code-block:: bash
mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads
mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double # Don't use any co-processors that might be available, use 2 OpenMP threads for each task, use double precision mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script
# Don't use any co-processors that might be available,
# use 2 OpenMP threads for each task, use double precision
mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script \
-pk intel 0 omp 2 mode double
Or run with the INTEL package by editing an input script Or run with the INTEL package by editing an input script
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@ -386,19 +391,19 @@ Long-Range Thread (LRT) mode is an option to the :doc:`package intel <package>`
with SMT. It generates an extra pthread for each MPI task. The thread with SMT. It generates an extra pthread for each MPI task. The thread
is dedicated to performing some of the PPPM calculations and MPI is dedicated to performing some of the PPPM calculations and MPI
communications. This feature requires setting the pre-processor flag communications. This feature requires setting the pre-processor flag
-DLMP_INTEL_USELRT in the makefile when compiling LAMMPS. It is unset ``-DLMP_INTEL_USELRT`` in the makefile when compiling LAMMPS. It is unset
in the default makefiles (\ *Makefile.mpi* and *Makefile.serial*\ ) but in the default makefiles (``Makefile.mpi`` and ``Makefile.serial``) but
it is set in all makefiles tuned for the INTEL package. On Intel it is set in all makefiles tuned for the INTEL package. On Intel
Xeon Phi x200 series CPUs, the LRT feature will likely improve Xeon Phi x200 series CPUs, the LRT feature will likely improve
performance, even on a single node. On Intel Xeon processors, using performance, even on a single node. On Intel Xeon processors, using
this mode might result in better performance when using multiple nodes, this mode might result in better performance when using multiple nodes,
depending on the specific machine configuration. To enable LRT mode, depending on the specific machine configuration. To enable LRT mode,
specify that the number of OpenMP threads is one less than would specify that the number of OpenMP threads is one less than would
normally be used for the run and add the "lrt yes" option to the "-pk" normally be used for the run and add the ``lrt yes`` option to the ``-pk``
command-line suffix or "package intel" command. For example, if a run command-line suffix or "package intel" command. For example, if a run
would normally perform best with "-pk intel 0 omp 4", instead use would normally perform best with "-pk intel 0 omp 4", instead use
"-pk intel 0 omp 3 lrt yes". When using LRT, you should set the ``-pk intel 0 omp 3 lrt yes``. When using LRT, you should set the
environment variable "KMP_AFFINITY=none". LRT mode is not supported environment variable ``KMP_AFFINITY=none``. LRT mode is not supported
when using offload. when using offload.
.. note:: .. note::
@ -411,12 +416,12 @@ Not all styles are supported in the INTEL package. You can mix
the INTEL package with styles from the :doc:`OPT <Speed_opt>` the INTEL package with styles from the :doc:`OPT <Speed_opt>`
package or the :doc:`OPENMP package <Speed_omp>`. Of course, this package or the :doc:`OPENMP package <Speed_omp>`. Of course, this
requires that these packages were installed at build time. This can requires that these packages were installed at build time. This can
performed automatically by using "-sf hybrid intel opt" or "-sf hybrid performed automatically by using ``-sf hybrid intel opt`` or ``-sf hybrid
intel omp" command-line options. Alternatively, the "opt" and "omp" intel omp`` command-line options. Alternatively, the "opt" and "omp"
suffixes can be appended manually in the input script. For the latter, suffixes can be appended manually in the input script. For the latter,
the :doc:`package omp <package>` command must be in the input script or the :doc:`package omp <package>` command must be in the input script or
the "-pk omp Nt" :doc:`command-line switch <Run_options>` must be used the ``-pk omp Nt`` :doc:`command-line switch <Run_options>` must be used
where Nt is the number of OpenMP threads. The number of OpenMP threads where ``Nt`` is the number of OpenMP threads. The number of OpenMP threads
should not be set differently for the different packages. Note that should not be set differently for the different packages. Note that
the :doc:`suffix hybrid intel omp <suffix>` command can also be used the :doc:`suffix hybrid intel omp <suffix>` command can also be used
within the input script to automatically append the "omp" suffix to within the input script to automatically append the "omp" suffix to
@ -436,7 +441,7 @@ alternative to LRT mode and the two cannot be used together.
Currently, when using Intel MPI with Intel Xeon Phi x200 series Currently, when using Intel MPI with Intel Xeon Phi x200 series
CPUs, better performance might be obtained by setting the CPUs, better performance might be obtained by setting the
environment variable "I_MPI_SHM_LMT=shm" for Linux kernels that do environment variable ``I_MPI_SHM_LMT=shm`` for Linux kernels that do
not yet have full support for AVX-512. Runs on Intel Xeon Phi x200 not yet have full support for AVX-512. Runs on Intel Xeon Phi x200
series processors will always perform better using MCDRAM. Please series processors will always perform better using MCDRAM. Please
consult your system documentation for the best approach to specify consult your system documentation for the best approach to specify
@ -515,7 +520,7 @@ per MPI task. Additionally, an offload timing summary is printed at
the end of each run. When offloading, the frequency for :doc:`atom sorting <atom_modify>` is changed to 1 so that the per-atom data is the end of each run. When offloading, the frequency for :doc:`atom sorting <atom_modify>` is changed to 1 so that the per-atom data is
effectively sorted at every rebuild of the neighbor lists. All the effectively sorted at every rebuild of the neighbor lists. All the
available co-processor threads on each Phi will be divided among MPI available co-processor threads on each Phi will be divided among MPI
tasks, unless the *tptask* option of the "-pk intel" :doc:`command-line switch <Run_options>` is used to limit the co-processor threads per tasks, unless the ``tptask`` option of the ``-pk intel`` :doc:`command-line switch <Run_options>` is used to limit the co-processor threads per
MPI task. MPI task.
Restrictions Restrictions

128
doc/src/Speed_kokkos.rst
View File

@ -48,7 +48,7 @@ version 23 November 2023 and Kokkos version 4.2.
Kokkos requires using a compiler that supports the c++17 standard. For Kokkos requires using a compiler that supports the c++17 standard. For
some compilers, it may be necessary to add a flag to enable c++17 support. some compilers, it may be necessary to add a flag to enable c++17 support.
For example, the GNU compiler uses the -std=c++17 flag. For a list of For example, the GNU compiler uses the ``-std=c++17`` flag. For a list of
compilers that have been tested with the Kokkos library, see the compilers that have been tested with the Kokkos library, see the
`requirements document of the Kokkos Wiki `requirements document of the Kokkos Wiki
<https://kokkos.github.io/kokkos-core-wiki/requirements.html>`_. <https://kokkos.github.io/kokkos-core-wiki/requirements.html>`_.
@ -111,14 +111,21 @@ for CPU acceleration, assuming one or more 16-core nodes.
.. code-block:: bash .. code-block:: bash
mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -in in.lj # 1 node, 16 MPI tasks/node, no multi-threading # 1 node, 16 MPI tasks/node, no multi-threading
mpirun -np 2 -ppn 1 lmp_kokkos_omp -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI task/node, 16 threads/task mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -in in.lj
mpirun -np 2 lmp_kokkos_omp -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 8 threads/task
mpirun -np 32 -ppn 4 lmp_kokkos_omp -k on t 4 -sf kk -in in.lj # 8 nodes, 4 MPI tasks/node, 4 threads/task
To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk # 2 nodes, 1 MPI task/node, 16 threads/task
kokkos" :doc:`command-line switches <Run_options>` in your mpirun mpirun -np 2 -ppn 1 lmp_kokkos_omp -k on t 16 -sf kk -in in.lj
command. You must use the "-k on" :doc:`command-line switch <Run_options>` to enable the KOKKOS package. It takes
# 1 node, 2 MPI tasks/node, 8 threads/task
mpirun -np 2 lmp_kokkos_omp -k on t 8 -sf kk -in in.lj
# 8 nodes, 4 MPI tasks/node, 4 threads/task
mpirun -np 32 -ppn 4 lmp_kokkos_omp -k on t 4 -sf kk -in in.lj
To run using the KOKKOS package, use the ``-k on``, ``-sf kk`` and ``-pk
kokkos`` :doc:`command-line switches <Run_options>` in your ``mpirun``
command. You must use the ``-k on`` :doc:`command-line switch <Run_options>` to enable the KOKKOS package. It takes
additional arguments for hardware settings appropriate to your system. additional arguments for hardware settings appropriate to your system.
For OpenMP use: For OpenMP use:
@ -126,18 +133,18 @@ For OpenMP use:
-k on t Nt -k on t Nt
The "t Nt" option specifies how many OpenMP threads per MPI task to The ``t Nt`` option specifies how many OpenMP threads per MPI task to
use with a node. The default is Nt = 1, which is MPI-only mode. Note use with a node. The default is ``Nt`` = 1, which is MPI-only mode. Note
that the product of MPI tasks \* OpenMP threads/task should not exceed that the product of MPI tasks \* OpenMP threads/task should not exceed
the physical number of cores (on a node), otherwise performance will the physical number of cores (on a node), otherwise performance will
suffer. If Hyper-Threading (HT) is enabled, then the product of MPI suffer. If Hyper-Threading (HT) is enabled, then the product of MPI
tasks \* OpenMP threads/task should not exceed the physical number of tasks \* OpenMP threads/task should not exceed the physical number of
cores \* hardware threads. The "-k on" switch also issues a cores \* hardware threads. The ``-k on`` switch also issues a
"package kokkos" command (with no additional arguments) which sets ``package kokkos`` command (with no additional arguments) which sets
various KOKKOS options to default values, as discussed on the various KOKKOS options to default values, as discussed on the
:doc:`package <package>` command doc page. :doc:`package <package>` command doc page.
The "-sf kk" :doc:`command-line switch <Run_options>` will automatically The ``-sf kk`` :doc:`command-line switch <Run_options>` will automatically
append the "/kk" suffix to styles that support it. In this manner no append the "/kk" suffix to styles that support it. In this manner no
modification to the input script is needed. Alternatively, one can run modification to the input script is needed. Alternatively, one can run
with the KOKKOS package by editing the input script as described with the KOKKOS package by editing the input script as described
@ -146,20 +153,22 @@ below.
.. note:: .. note::
When using a single OpenMP thread, the Kokkos Serial back end (i.e. When using a single OpenMP thread, the Kokkos Serial back end (i.e.
Makefile.kokkos_mpi_only) will give better performance than the OpenMP ``Makefile.kokkos_mpi_only``) will give better performance than the OpenMP
back end (i.e. Makefile.kokkos_omp) because some of the overhead to make back end (i.e. ``Makefile.kokkos_omp``) because some of the overhead to make
the code thread-safe is removed. the code thread-safe is removed.
.. note:: .. note::
Use the "-pk kokkos" :doc:`command-line switch <Run_options>` to Use the ``-pk kokkos`` :doc:`command-line switch <Run_options>` to
change the default :doc:`package kokkos <package>` options. See its doc change the default :doc:`package kokkos <package>` options. See its doc
page for details and default settings. Experimenting with its options page for details and default settings. Experimenting with its options
can provide a speed-up for specific calculations. For example: can provide a speed-up for specific calculations. For example:
.. code-block:: bash .. code-block:: bash
mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj # Newton on, Half neighbor list, non-threaded comm # Newton on, Half neighbor list, non-threaded comm
mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk \
-pk kokkos newton on neigh half comm no -in in.lj
If the :doc:`newton <newton>` command is used in the input If the :doc:`newton <newton>` command is used in the input
script, it can also override the Newton flag defaults. script, it can also override the Newton flag defaults.
@ -172,7 +181,7 @@ small numbers of threads (i.e. 8 or less) but does increase memory
footprint and is not scalable to large numbers of threads. An footprint and is not scalable to large numbers of threads. An
alternative to data duplication is to use thread-level atomic operations alternative to data duplication is to use thread-level atomic operations
which do not require data duplication. The use of atomic operations can which do not require data duplication. The use of atomic operations can
be enforced by compiling LAMMPS with the "-DLMP_KOKKOS_USE_ATOMICS" be enforced by compiling LAMMPS with the ``-DLMP_KOKKOS_USE_ATOMICS``
pre-processor flag. Most but not all Kokkos-enabled pair_styles support pre-processor flag. Most but not all Kokkos-enabled pair_styles support
data duplication. Alternatively, full neighbor lists avoid the need for data duplication. Alternatively, full neighbor lists avoid the need for
duplication or atomic operations but require more compute operations per duplication or atomic operations but require more compute operations per
@ -190,10 +199,13 @@ they do not migrate during a simulation.
If you are not certain MPI tasks are being bound (check the defaults If you are not certain MPI tasks are being bound (check the defaults
for your MPI installation), binding can be forced with these flags: for your MPI installation), binding can be forced with these flags:
.. parsed-literal:: .. code-block:: bash
OpenMPI 1.8: mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ... # OpenMPI 1.8
Mvapich2 2.0: mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ... mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ...
# Mvapich2 2.0
mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ...
For binding threads with KOKKOS OpenMP, use thread affinity environment For binding threads with KOKKOS OpenMP, use thread affinity environment
variables to force binding. With OpenMP 3.1 (gcc 4.7 or later, intel 12 variables to force binding. With OpenMP 3.1 (gcc 4.7 or later, intel 12
@ -222,15 +234,24 @@ Examples of mpirun commands that follow these rules are shown below.
.. code-block:: bash .. code-block:: bash
# Running on an Intel KNL node with 68 cores (272 threads/node via 4x hardware threading): # Running on an Intel KNL node with 68 cores
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj # 1 node, 64 MPI tasks/node, 4 threads/task # (272 threads/node via 4x hardware threading):
mpirun -np 66 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj # 1 node, 66 MPI tasks/node, 4 threads/task
mpirun -np 32 lmp_kokkos_phi -k on t 8 -sf kk -in in.lj # 1 node, 32 MPI tasks/node, 8 threads/task
mpirun -np 512 -ppn 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj # 8 nodes, 64 MPI tasks/node, 4 threads/task
The -np setting of the mpirun command sets the number of MPI # 1 node, 64 MPI tasks/node, 4 threads/task
tasks/node. The "-k on t Nt" command-line switch sets the number of mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj
threads/task as Nt. The product of these two values should be N, i.e.
# 1 node, 66 MPI tasks/node, 4 threads/task
mpirun -np 66 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj
# 1 node, 32 MPI tasks/node, 8 threads/task
mpirun -np 32 lmp_kokkos_phi -k on t 8 -sf kk -in in.lj
# 8 nodes, 64 MPI tasks/node, 4 threads/task
mpirun -np 512 -ppn 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj
The ``-np`` setting of the mpirun command sets the number of MPI
tasks/node. The ``-k on t Nt`` command-line switch sets the number of
threads/task as ``Nt``. The product of these two values should be N, i.e.
256 or 264. 256 or 264.
.. note:: .. note::
@ -240,7 +261,7 @@ threads/task as Nt. The product of these two values should be N, i.e.
flag to "on" for both pairwise and bonded interactions. This will flag to "on" for both pairwise and bonded interactions. This will
typically be best for many-body potentials. For simpler pairwise typically be best for many-body potentials. For simpler pairwise
potentials, it may be faster to use a "full" neighbor list with potentials, it may be faster to use a "full" neighbor list with
Newton flag to "off". Use the "-pk kokkos" :doc:`command-line switch Newton flag to "off". Use the ``-pk kokkos`` :doc:`command-line switch
<Run_options>` to change the default :doc:`package kokkos <package>` <Run_options>` to change the default :doc:`package kokkos <package>`
options. See its documentation page for details and default options. See its documentation page for details and default
settings. Experimenting with its options can provide a speed-up for settings. Experimenting with its options can provide a speed-up for
@ -248,8 +269,12 @@ threads/task as Nt. The product of these two values should be N, i.e.
.. code-block:: bash .. code-block:: bash
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm host -in in.reax # Newton on, half neighbor list, threaded comm # Newton on, half neighbor list, threaded comm
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton off neigh full comm no -in in.lj # Newton off, full neighbor list, non-threaded comm mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm host -in in.reax
# Newton off, full neighbor list, non-threaded comm
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk \
-pk kokkos newton off neigh full comm no -in in.lj
.. note:: .. note::
@ -266,8 +291,8 @@ threads/task as Nt. The product of these two values should be N, i.e.
Running on GPUs Running on GPUs
^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^
Use the "-k" :doc:`command-line switch <Run_options>` to specify the Use the ``-k`` :doc:`command-line switch <Run_options>` to specify the
number of GPUs per node. Typically the -np setting of the mpirun command number of GPUs per node. Typically the ``-np`` setting of the ``mpirun`` command
should set the number of MPI tasks/node to be equal to the number of should set the number of MPI tasks/node to be equal to the number of
physical GPUs on the node. You can assign multiple MPI tasks to the same physical GPUs on the node. You can assign multiple MPI tasks to the same
GPU with the KOKKOS package, but this is usually only faster if some GPU with the KOKKOS package, but this is usually only faster if some
@ -290,8 +315,11 @@ one or more nodes, each with two GPUs:
.. code-block:: bash .. code-block:: bash
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 2 GPUs/node # 1 node, 2 MPI tasks/node, 2 GPUs/node
mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total) mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj
# 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total)
mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj
.. note:: .. note::
@ -303,7 +331,7 @@ one or more nodes, each with two GPUs:
neighbor lists and setting the Newton flag to "on" may be faster. For neighbor lists and setting the Newton flag to "on" may be faster. For
many pair styles, setting the neighbor binsize equal to twice the CPU many pair styles, setting the neighbor binsize equal to twice the CPU
default value will give speedup, which is the default when running on default value will give speedup, which is the default when running on
GPUs. Use the "-pk kokkos" :doc:`command-line switch <Run_options>` GPUs. Use the ``-pk kokkos`` :doc:`command-line switch <Run_options>`
to change the default :doc:`package kokkos <package>` options. See to change the default :doc:`package kokkos <package>` options. See
its documentation page for details and default its documentation page for details and default
settings. Experimenting with its options can provide a speed-up for settings. Experimenting with its options can provide a speed-up for
@ -311,7 +339,9 @@ one or more nodes, each with two GPUs:
.. code-block:: bash .. code-block:: bash
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighbor list, set binsize = neighbor ghost cutoff # Newton on, half neighbor list, set binsize = neighbor ghost cutoff
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk \
-pk kokkos newton on neigh half binsize 2.8 -in in.lj
.. note:: .. note::
@ -329,7 +359,7 @@ one or more nodes, each with two GPUs:
more), the creation of the atom map (required for molecular systems) more), the creation of the atom map (required for molecular systems)
on the GPU can slow down significantly or run out of GPU memory and on the GPU can slow down significantly or run out of GPU memory and
thus slow down the whole calculation or cause a crash. You can use thus slow down the whole calculation or cause a crash. You can use
the "-pk kokkos atom/map no" :doc:`command-line switch <Run_options>` the ``-pk kokkos atom/map no`` :doc:`command-line switch <Run_options>`
of the :doc:`package kokkos atom/map no <package>` command to create of the :doc:`package kokkos atom/map no <package>` command to create
the atom map on the CPU instead. the atom map on the CPU instead.
@ -346,20 +376,20 @@ one or more nodes, each with two GPUs:
.. note:: .. note::
To get an accurate timing breakdown between time spend in pair, To get an accurate timing breakdown between time spend in pair,
kspace, etc., you must set the environment variable CUDA_LAUNCH_BLOCKING=1. kspace, etc., you must set the environment variable ``CUDA_LAUNCH_BLOCKING=1``.
However, this will reduce performance and is not recommended for production runs. However, this will reduce performance and is not recommended for production runs.
Run with the KOKKOS package by editing an input script Run with the KOKKOS package by editing an input script
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Alternatively the effect of the "-sf" or "-pk" switches can be Alternatively the effect of the ``-sf`` or ``-pk`` switches can be
duplicated by adding the :doc:`package kokkos <package>` or :doc:`suffix kk <suffix>` commands to your input script. duplicated by adding the :doc:`package kokkos <package>` or :doc:`suffix kk <suffix>` commands to your input script.
The discussion above for building LAMMPS with the KOKKOS package, the The discussion above for building LAMMPS with the KOKKOS package, the
``mpirun`` or ``mpiexec`` command, and setting appropriate thread ``mpirun`` or ``mpiexec`` command, and setting appropriate thread
properties are the same. properties are the same.
You must still use the "-k on" :doc:`command-line switch <Run_options>` You must still use the ``-k on`` :doc:`command-line switch <Run_options>`
to enable the KOKKOS package, and specify its additional arguments for to enable the KOKKOS package, and specify its additional arguments for
hardware options appropriate to your system, as documented above. hardware options appropriate to your system, as documented above.
@ -378,7 +408,7 @@ wish to change any of its option defaults, as set by the "-k on"
With the KOKKOS package, both OpenMP multi-threading and GPUs can be With the KOKKOS package, both OpenMP multi-threading and GPUs can be
compiled and used together in a few special cases. In the makefile for compiled and used together in a few special cases. In the makefile for
the conventional build, the KOKKOS_DEVICES variable must include both, the conventional build, the ``KOKKOS_DEVICES`` variable must include both,
"Cuda" and "OpenMP", as is the case for ``/src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi``. "Cuda" and "OpenMP", as is the case for ``/src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi``.
.. code-block:: bash .. code-block:: bash
@ -390,14 +420,14 @@ in the ``kokkos-cuda.cmake`` CMake preset file.
.. code-block:: bash .. code-block:: bash
cmake ../cmake -DKokkos_ENABLE_CUDA=yes -DKokkos_ENABLE_OPENMP=yes cmake -DKokkos_ENABLE_CUDA=yes -DKokkos_ENABLE_OPENMP=yes ../cmake
The suffix "/kk" is equivalent to "/kk/device", and for Kokkos CUDA, The suffix "/kk" is equivalent to "/kk/device", and for Kokkos CUDA,
using the "-sf kk" in the command line gives the default CUDA version using the ``-sf kk`` in the command line gives the default CUDA version
everywhere. However, if the "/kk/host" suffix is added to a specific everywhere. However, if the "/kk/host" suffix is added to a specific
style in the input script, the Kokkos OpenMP (CPU) version of that style in the input script, the Kokkos OpenMP (CPU) version of that
specific style will be used instead. Set the number of OpenMP threads specific style will be used instead. Set the number of OpenMP threads
as "t Nt" and the number of GPUs as "g Ng" as ``t Nt`` and the number of GPUs as ``g Ng``
.. parsed-literal:: .. parsed-literal::
@ -409,7 +439,7 @@ For example, the command to run with 1 GPU and 8 OpenMP threads is then:
mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk
Conversely, if the "-sf kk/host" is used in the command line and then Conversely, if the ``-sf kk/host`` is used in the command line and then
the "/kk" or "/kk/device" suffix is added to a specific style in your the "/kk" or "/kk/device" suffix is added to a specific style in your
input script, then only that specific style will run on the GPU while input script, then only that specific style will run on the GPU while
everything else will run on the CPU in OpenMP mode. Note that the everything else will run on the CPU in OpenMP mode. Note that the
@ -418,11 +448,11 @@ special case:
A kspace style and/or molecular topology (bonds, angles, etc.) running A kspace style and/or molecular topology (bonds, angles, etc.) running
on the host CPU can overlap with a pair style running on the on the host CPU can overlap with a pair style running on the
GPU. First compile with "--default-stream per-thread" added to CCFLAGS GPU. First compile with ``--default-stream per-thread`` added to ``CCFLAGS``
in the Kokkos CUDA Makefile. Then explicitly use the "/kk/host" in the Kokkos CUDA Makefile. Then explicitly use the "/kk/host"
suffix for kspace and bonds, angles, etc. in the input file and the suffix for kspace and bonds, angles, etc. in the input file and the
"kk" suffix (equal to "kk/device") on the command line. Also make "kk" suffix (equal to "kk/device") on the command line. Also make
sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1" sure the environment variable ``CUDA_LAUNCH_BLOCKING`` is not set to "1"
so CPU/GPU overlap can occur. so CPU/GPU overlap can occur.
Performance to expect Performance to expect

29
doc/src/Speed_omp.rst
View File

@ -28,32 +28,39 @@ These examples assume one or more 16-core nodes.
.. code-block:: bash .. code-block:: bash
env OMP_NUM_THREADS=16 lmp_omp -sf omp -in in.script # 1 MPI task, 16 threads according to OMP_NUM_THREADS # 1 MPI task, 16 threads according to OMP_NUM_THREADS
lmp_mpi -sf omp -in in.script # 1 MPI task, no threads, optimized kernels env OMP_NUM_THREADS=16 lmp_omp -sf omp -in in.script
mpirun -np 4 lmp_omp -sf omp -pk omp 4 -in in.script # 4 MPI tasks, 4 threads/task
mpirun -np 32 -ppn 4 lmp_omp -sf omp -pk omp 4 -in in.script # 8 nodes, 4 MPI tasks/node, 4 threads/task # 1 MPI task, no threads, optimized kernels
lmp_mpi -sf omp -in in.script
# 4 MPI tasks, 4 threads/task
mpirun -np 4 lmp_omp -sf omp -pk omp 4 -in in.script
# 8 nodes, 4 MPI tasks/node, 4 threads/task
mpirun -np 32 -ppn 4 lmp_omp -sf omp -pk omp 4 -in in.script
The ``mpirun`` or ``mpiexec`` command sets the total number of MPI tasks The ``mpirun`` or ``mpiexec`` command sets the total number of MPI tasks
used by LAMMPS (one or multiple per compute node) and the number of MPI used by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via tasks used per node. E.g. the mpirun command in MPICH does this via
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode. its ``-np`` and ``-ppn`` switches. Ditto for OpenMPI via ``-np`` and ``-npernode``.
You need to choose how many OpenMP threads per MPI task will be used You need to choose how many OpenMP threads per MPI task will be used
by the OPENMP package. Note that the product of MPI tasks \* by the OPENMP package. Note that the product of MPI tasks \*
threads/task should not exceed the physical number of cores (on a threads/task should not exceed the physical number of cores (on a
node), otherwise performance will suffer. node), otherwise performance will suffer.
As in the lines above, use the "-sf omp" :doc:`command-line switch <Run_options>`, which will automatically append "omp" to As in the lines above, use the ``-sf omp`` :doc:`command-line switch <Run_options>`, which will automatically append "omp" to
styles that support it. The "-sf omp" switch also issues a default styles that support it. The ``-sf omp`` switch also issues a default
:doc:`package omp 0 <package>` command, which will set the number of :doc:`package omp 0 <package>` command, which will set the number of
threads per MPI task via the OMP_NUM_THREADS environment variable. threads per MPI task via the ``OMP_NUM_THREADS`` environment variable.
You can also use the "-pk omp Nt" :doc:`command-line switch <Run_options>`, to explicitly set Nt = # of OpenMP threads You can also use the ``-pk omp Nt`` :doc:`command-line switch <Run_options>`, to explicitly set ``Nt`` = # of OpenMP threads
per MPI task to use, as well as additional options. Its syntax is the per MPI task to use, as well as additional options. Its syntax is the
same as the :doc:`package omp <package>` command whose page gives same as the :doc:`package omp <package>` command whose page gives
details, including the default values used if it is not specified. It details, including the default values used if it is not specified. It
also gives more details on how to set the number of threads via the also gives more details on how to set the number of threads via the
OMP_NUM_THREADS environment variable. ``OMP_NUM_THREADS`` environment variable.
Or run with the OPENMP package by editing an input script Or run with the OPENMP package by editing an input script
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@ -71,7 +78,7 @@ Use the :doc:`suffix omp <suffix>` command, or you can explicitly add an
You must also use the :doc:`package omp <package>` command to enable the You must also use the :doc:`package omp <package>` command to enable the
OPENMP package. When you do this you also specify how many threads OPENMP package. When you do this you also specify how many threads
per MPI task to use. The command page explains other options and per MPI task to use. The command page explains other options and
how to set the number of threads via the OMP_NUM_THREADS environment how to set the number of threads via the ``OMP_NUM_THREADS`` environment
variable. variable.
Speed-up to expect Speed-up to expect

41
doc/src/Speed_packages.rst
View File

@ -80,23 +80,30 @@ it provides, follow these general steps. Details vary from package to
package and are explained in the individual accelerator doc pages, package and are explained in the individual accelerator doc pages,
listed above: listed above:
+--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ +-----------------------------------------------------------+---------------------------------------------+
| build the accelerator library | only for GPU package | | build the accelerator library | only for GPU package |
+--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ +-----------------------------------------------------------+---------------------------------------------+
| install the accelerator package | make yes-opt, make yes-intel, etc | | install the accelerator package | ``make yes-opt``, ``make yes-intel``, etc |
+--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ +-----------------------------------------------------------+---------------------------------------------+
| add compile/link flags to Makefile.machine in src/MAKE | only for INTEL, KOKKOS, OPENMP, OPT packages | | add compile/link flags to ``Makefile.machine`` | only for INTEL, KOKKOS, OPENMP, |
+--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ | in ``src/MAKE`` | OPT packages |
| re-build LAMMPS | make machine | +-----------------------------------------------------------+---------------------------------------------+
+--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ | re-build LAMMPS | ``make machine`` |
| prepare and test a regular LAMMPS simulation | lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script | +-----------------------------------------------------------+---------------------------------------------+
+--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ | prepare and test a regular LAMMPS simulation | ``lmp_machine -in in.script;`` |
| enable specific accelerator support via '-k on' :doc:`command-line switch <Run_options>`, | only needed for KOKKOS package | | | ``mpirun -np 32 lmp_machine -in in.script`` |
+--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ +-----------------------------------------------------------+---------------------------------------------+
| set any needed options for the package via "-pk" :doc:`command-line switch <Run_options>` or :doc:`package <package>` command, | only if defaults need to be changed | | enable specific accelerator support via ``-k on`` | only needed for KOKKOS package |
+--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ | :doc:`command-line switch <Run_options>` | |
| use accelerated styles in your input via "-sf" :doc:`command-line switch <Run_options>` or :doc:`suffix <suffix>` command | lmp_machine -in in.script -sf gpu | +-----------------------------------------------------------+---------------------------------------------+
+--------------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------+ | set any needed options for the package via ``-pk`` | only if defaults need to be changed |
| :doc:`command-line switch <Run_options>` or | |
| :doc:`package <package>` command | |
+-----------------------------------------------------------+---------------------------------------------+
| use accelerated styles in your input via ``-sf`` | ``lmp_machine -in in.script -sf gpu`` |
| :doc:`command-line switch <Run_options>` or | |
| :doc:`suffix <suffix>` command | |
+-----------------------------------------------------------+---------------------------------------------+
Note that the first 4 steps can be done as a single command with Note that the first 4 steps can be done as a single command with
suitable make command invocations. This is discussed on the suitable make command invocations. This is discussed on the

15
doc/utils/sphinx-config/conf.py.in
View File

@ -275,12 +275,17 @@ else:
mathjax_path = 'mathjax/es5/tex-mml-chtml.js' mathjax_path = 'mathjax/es5/tex-mml-chtml.js'
# hack to enable use of \AA in :math: # hack to enable use of \AA in :math:
# add :lammps: role for inline LAMMPS code highlight
rst_prolog = r""" rst_prolog = r"""
.. only:: html .. only:: html
:math:`\renewcommand{\AA}{\text{Å}}` :math:`\renewcommand{\AA}{\text{Å}}`
.. role:: lammps(code)
:language: LAMMPS
:class: highlight
""" """
# -- Options for LaTeX output --------------------------------------------- # -- Options for LaTeX output ---------------------------------------------
@ -294,6 +299,8 @@ latex_elements = {
# Additional stuff for the LaTeX preamble. # Additional stuff for the LaTeX preamble.
'preamble': r''' 'preamble': r'''
\usepackage{afterpage}
\usepackage{xcolor}
\setcounter{tocdepth}{2} \setcounter{tocdepth}{2}
\renewcommand{\sfdefault}{ptm} % Use Times New Roman font for \textrm \renewcommand{\sfdefault}{ptm} % Use Times New Roman font for \textrm
\renewcommand{\sfdefault}{phv} % Use Helvetica font for \textsf \renewcommand{\sfdefault}{phv} % Use Helvetica font for \textsf
@ -339,7 +346,13 @@ latex_elements = {
\renewcommand*\l@subsection{\@dottedtocline{2}{4.6em}{4.5em}} \renewcommand*\l@subsection{\@dottedtocline{2}{4.6em}{4.5em}}
} }
\makeatother \makeatother
''' ''',
'maketitle': r'''
\pagecolor{black}
\color{white}
\afterpage{\nopagecolor\color{black}}
\sphinxmaketitle
''',
} }
# copy custom style file for tweaking index layout # copy custom style file for tweaking index layout