forked from lijiext/lammps
Merge branch 'master' into collected-small-changes
This commit is contained in:
Axel Kohlmeyer
commit
ceed9284c1
|
|
@ -248,6 +248,26 @@ if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
|
|||
endif()
|
||||
endif()
|
||||
|
||||
#######################################
|
||||
# add custom target for IWYU analysis
|
||||
#######################################
|
||||
set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool")
|
||||
mark_as_advanced(ENABLE_IWYU)
|
||||
if(ENABLE_IWYU)
|
||||
find_program(IWYU_EXE NAMES include-what-you-use iwyu)
|
||||
find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py)
|
||||
if (IWYU_EXE AND IWYU_TOOL)
|
||||
add_custom_target(
|
||||
iwyu
|
||||
${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp
|
||||
COMMENT "Running IWYU")
|
||||
add_dependencies(iwyu lammps)
|
||||
else()
|
||||
message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable"
|
||||
"and the iwyu-tool/iwyu_tool script installed in your PATH")
|
||||
endif()
|
||||
endif()
|
||||
|
||||
set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
|
||||
mark_as_advanced(ENABLE_SANITIZER)
|
||||
set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
|
||||
|
|
@ -292,7 +312,6 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
|
|||
endif()
|
||||
endif()
|
||||
|
||||
|
||||
find_package(JPEG QUIET)
|
||||
option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND})
|
||||
if(WITH_JPEG)
|
||||
|
|
|
|||
|
|
@ -0,0 +1,7 @@
|
|||
[
|
||||
{ include: [ "<bits/types/struct_rusage.h>", private, "<sys/resource.h>", public ] },
|
||||
{ include: [ "<bits/exception.h>", public, "<exception>", public ] },
|
||||
{ include: [ "@<Eigen/.*>", private, "<Eigen/Eigen>", public ] },
|
||||
{ include: [ "@<gtest/.*>", private, "\"gtest/gtest.h\"", public ] },
|
||||
{ include: [ "@<gmock/.*>", private, "\"gmock/gmock.h\"", public ] },
|
||||
]
|
||||
|
|
@ -91,32 +91,31 @@ statements should follow the "include what you use" principle.
|
|||
|
||||
Include files should be included in this order:
|
||||
* the header matching the implementation (`some_class.h` for file `some_class.cpp`)
|
||||
* mpi.h
|
||||
* system and library headers (anything that is using angular brackets; C-library headers first, then C++)
|
||||
* mpi.h (only if needed)
|
||||
* LAMMPS local headers (preferably in alphabetical order)
|
||||
* system and library headers (anything that is using angular brackets; preferably in alphabetical order)
|
||||
* conditional include statements (i.e. anything bracketed with ifdefs)
|
||||
|
||||
### Special Cases and Exceptions
|
||||
|
||||
#### pointers.h
|
||||
|
||||
The `pointer.h` header file also includes `cstdio`, `cstddef`,
|
||||
`string`, `lmptype.h`, and `utils.h` (and through those indirectly
|
||||
`stdint.h`, `intttypes.h`, cstdlib, and `climits`).
|
||||
The `pointer.h` header file also includes (in this order) `lmptype.h`,
|
||||
`mpi.h`, `cstddef`, `cstdio`, `string`, `utils.h`, and `fmt/format.h`
|
||||
and through `lmptype.h` indirectly also `climits`, `cstdlib`, `cinttypes`.
|
||||
This means any header including `pointers.h` can assume that `FILE`,
|
||||
`NULL`, `INT_MAX` are defined, they may freely use std::string
|
||||
and functions from the utils namespace without including the
|
||||
corresponding header files.
|
||||
`NULL`, `INT_MAX` are defined, and the may freely use the std::string
|
||||
for arguments. Corresponding implementation files do not need to include
|
||||
those headers.
|
||||
|
||||
## Tools
|
||||
|
||||
The [Include What You Use tool](https://include-what-you-use.org/)
|
||||
can be used to provide supporting information about compliance with
|
||||
the rules listed here. There are some limitations and the IWYU tool
|
||||
may give incorrect advice. The tools is activated by setting the
|
||||
CMake variable `CMAKE_CXX_INCLUDE_WHAT_YOU_USE` variable to the
|
||||
path of the `include-what-you-use` command. When activated, the
|
||||
tool will be run after each compilation and provide suggestions for
|
||||
which include files should be added or removed.
|
||||
the rules listed here. Through setting `-DENABLE_IWYU=on` when running
|
||||
CMake, a custom build target is added that will enable recording
|
||||
the compilation commands and then run the `iwyu_tool` using the
|
||||
recorded compilation commands information when typing `make iwyu`.
|
||||
|
||||
## Legacy Code
|
||||
|
||||
|
|
|
|||
|
|
@ -115,12 +115,12 @@ self-installed MPICH or OpenMPI, so you should study the provided
|
|||
documentation to find out how to build and link with it.
|
||||
|
||||
The majority of OpenMP (threading) support in LAMMPS is provided by the
|
||||
``USER-OMP`` package; see the :doc:`Speed omp <Speed_omp>` doc page for
|
||||
details. The ``USER-INTEL`` package also includes OpenMP threading (it
|
||||
is compatible with ``USER-OMP`` and will usually fall back on styles
|
||||
from that package, if a ``USER-INTEL`` does not exist) and adds
|
||||
vectorization support when compiled with compatible compilers, in
|
||||
particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS``
|
||||
``USER-OMP`` package; see the :doc:`Speed_omp`
|
||||
page for details. The ``USER-INTEL`` package also includes OpenMP
|
||||
threading (it is compatible with ``USER-OMP`` and will usually fall
|
||||
back on styles from that package, if a ``USER-INTEL`` does not exist)
|
||||
and adds vectorization support when compiled with compatible compilers,
|
||||
in particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS``
|
||||
package can be compiled to include OpenMP threading.
|
||||
|
||||
In addition, there are a few commands in LAMMPS that have native OpenMP
|
||||
|
|
@ -290,13 +290,13 @@ Serial build with GNU gcc (see ``src/MAKE/Makefile.serial``):
|
|||
compiler that supports C++11; either as a binary package or through
|
||||
compiling from source.
|
||||
|
||||
If you build LAMMPS with any :doc:`accelerator packages
|
||||
<Speed_packages>` included, there may be specific optimization flags
|
||||
If you build LAMMPS with any :doc:`Speed_packages` included, there may
|
||||
be specific compiler or linker flags
|
||||
that are either required or recommended to enable required features and
|
||||
to achieve optimal performance. You need to include these in the
|
||||
CCFLAGS and LINKFLAGS settings above. For details, see the individual
|
||||
package doc pages listed on the :doc:`Speed packages <Speed_packages>`
|
||||
doc page. Or examine these files in the src/MAKE/OPTIONS directory.
|
||||
package doc pages listed on the :doc:`Speed_packages`
|
||||
page. Or examine these files in the src/MAKE/OPTIONS directory.
|
||||
They correspond to each of the 5 accelerator packages and their hardware
|
||||
variants:
|
||||
|
||||
|
|
@ -418,7 +418,7 @@ recommended to ensure the integrity of the system software installation.
|
|||
|
||||
.. _debug:
|
||||
|
||||
Excluding or removing debug support
|
||||
Including or removing debug support
|
||||
-----------------------------------
|
||||
|
||||
By default the compilation settings will include the *-g* flag which
|
||||
|
|
@ -460,7 +460,7 @@ python packages are installed into that virtual environment via the pip
|
|||
tool. The actual translation is then done via make commands.
|
||||
|
||||
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
|
||||
.. _sphinx: https://sphinx-doc.org
|
||||
.. _sphinx: https://www.sphinx-doc.org
|
||||
|
||||
Documentation make option
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
|
|
|||
|
|
@ -28,6 +28,40 @@ variable VERBOSE set to 1:
|
|||
|
||||
----------
|
||||
|
||||
.. _iwyu_processing:
|
||||
|
||||
Report missing and unneeded '#include' statements
|
||||
-------------------------------------------------
|
||||
|
||||
The conventions for how and when to use and order include statements in
|
||||
LAMMPS are `documented in a separate file <https://github.com/lammps/lammps/blob/master/doc/include-file-conventions.md>`_
|
||||
(also included in the source code distribution). To assist with following
|
||||
these conventions one can use the `Include What You Use tool <https://include-what-you-use.org/>`_.
|
||||
This is still under development and for large and complex projects like LAMMPS
|
||||
there are some false positives, so suggested changes need to be verified manually.
|
||||
It is recommended to use at least version 0.14, which has much fewer incorrect
|
||||
reports than earlier versions.
|
||||
|
||||
The necessary steps to generate the report can be enabled via a
|
||||
CMake variable:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
-D ENABLE_IWYU=value # value = no (default) or yes
|
||||
|
||||
This will check if the required binary (include-what-you-use or iwyu)
|
||||
and python script script (iwyu-tool or iwyu_tool or iwyu_tool.py) can
|
||||
be found in the path. The analysis can then be started with:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
make iwyu
|
||||
|
||||
This may first run some compilation, as the analysis is dependent
|
||||
on recording all commands required to do the compilation.
|
||||
|
||||
----------
|
||||
|
||||
.. _sanitizer:
|
||||
|
||||
Address, Undefined Behavior, and Thread Sanitizer Support
|
||||
|
|
@ -37,14 +71,14 @@ Compilers such as GCC and Clang support generating instrumented binaries
|
|||
which use different sanitizer libraries to detect problems in the code
|
||||
during run-time. They can detect issues like:
|
||||
|
||||
- `memory leaks <https://clang.llvm.org/docs/AddressSanitizer.html>`_
|
||||
- `memory leaks <https://clang.llvm.org/docs/AddressSanitizer.html#memory-leak-detection>`_
|
||||
- `undefined behavior <https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html>`_
|
||||
- `data races <https://clang.llvm.org/docs/ThreadSanitizer.html>`_
|
||||
|
||||
Please note that this kind of instrumentation usually comes with a
|
||||
performance hit (but much less than using tools like `Valgrind
|
||||
<https://valgrind.org>`_ with a more low level approach). The to enable
|
||||
these features additional compiler flags need to be added to the
|
||||
<https://valgrind.org>`_ with a more low level approach). To enable
|
||||
these features, additional compiler flags need to be added to the
|
||||
compilation and linking stages. This is done through setting the
|
||||
``ENABLE_SANITIZER`` variable during configuration. Examples:
|
||||
|
||||
|
|
@ -77,7 +111,7 @@ error margin). The status of this automated testing can be viewed on
|
|||
The unit testing facility is integrated into the CMake build process
|
||||
of the LAMMPS source code distribution itself. It can be enabled by
|
||||
setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
|
||||
It requires the `YAML <http://pyyaml.org/>`_ library and development
|
||||
It requires the `PyYAML <http://pyyaml.org/>`_ library and development
|
||||
headers to compile and will download and compile a recent version of the
|
||||
`Googletest <https://github.com/google/googletest/>`_ C++ test framework
|
||||
for implementing the tests.
|
||||
|
|
|
|||
|
|
@ -234,11 +234,10 @@ command, you also need to have libcurl installed with the matching
|
|||
development headers and the curl-config tool.
|
||||
|
||||
If you would like to use the :doc:`kim_property <kim_commands>`
|
||||
command, you need to build LAMMPS with the Python 3.6 or later package
|
||||
installed. See the :doc:`Python <python>` doc page for more info on building
|
||||
LAMMPS with the version of Python on your system.
|
||||
After successfully building LAMMPS with Python, you need to
|
||||
install the kim-property Python package, which can be easily done using
|
||||
command, you need to build LAMMPS with the PYTHON package installed
|
||||
and linked to Python 3.6 or later. See the :ref:`PYTHON package build info <python>`
|
||||
for more details on this. After successfully building LAMMPS with Python, you
|
||||
also need to install the kim-property Python package, which can be easily done using
|
||||
*pip* as ``pip install kim-property``, or from the *conda-forge* channel as
|
||||
``conda install kim-property`` if LAMMPS is built in Conda. More detailed
|
||||
information is available at:
|
||||
|
|
@ -812,10 +811,11 @@ a corresponding ``Makefile.lammps.machine`` file.
|
|||
PYTHON package
|
||||
---------------------------
|
||||
|
||||
Building with the PYTHON package requires you have a Python shared
|
||||
library available on your system, which needs to be a Python 2.7
|
||||
version or a Python 3.x version. See ``lib/python/README`` for more
|
||||
details.
|
||||
Building with the PYTHON package requires you have a the Python development
|
||||
headers and library available on your system, which needs to be a Python 2.7
|
||||
version or a Python 3.x version. Since support for Python 2.x has ended,
|
||||
using Python 3.x is strongly recommended. See ``lib/python/README`` for
|
||||
additional details.
|
||||
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
|
@ -1095,7 +1095,7 @@ USER-PLUMED package
|
|||
|
||||
Before building LAMMPS with this package, you must first build PLUMED.
|
||||
PLUMED can be built as part of the LAMMPS build or installed separately
|
||||
from LAMMPS using the generic `plumed installation instructions <plumedinstall_>`_.
|
||||
from LAMMPS using the generic `PLUMED installation instructions <plumedinstall_>`_.
|
||||
The USER-PLUMED package has been tested to work with Plumed versions
|
||||
2.4.x, 2.5.x, and 2.6.x and will error out, when trying to run calculations
|
||||
with a different version of the Plumed kernel.
|
||||
|
|
@ -1262,7 +1262,7 @@ To build with this package, you must choose which hardware you want to
|
|||
build for, either x86 CPUs or Intel KNLs in offload mode. You should
|
||||
also typically :ref:`install the USER-OMP package <user-omp>`, as it can be
|
||||
used in tandem with the USER-INTEL package to good effect, as explained
|
||||
on the :doc:`Speed intel <Speed_intel>` doc page.
|
||||
on the :doc:`Speed_intel` page.
|
||||
|
||||
When using Intel compilers version 16.0 or later is required. You can
|
||||
also use the GNU or Clang compilers and they will provide performance
|
||||
|
|
|
|||
|
|
@ -4,11 +4,11 @@ Link LAMMPS as a library to another code
|
|||
LAMMPS is designed as a library of C++ objects that can be
|
||||
integrated into other applications including Python scripts.
|
||||
The files ``src/library.cpp`` and ``src/library.h`` define a
|
||||
C-style API for using LAMMPS as a library. See the :doc:`Howto
|
||||
library <Howto_library>` page for a description of the interface
|
||||
and how to use it for your needs.
|
||||
C-style API for using LAMMPS as a library. See the
|
||||
:doc:`Howto_library` page
|
||||
for a description of the interface and how to use it for your needs.
|
||||
|
||||
The :doc:`Build basics <Build_basics>` doc page explains how to build
|
||||
The :doc:`Build_basics` page explains how to build
|
||||
LAMMPS as either a shared or static library. This results in a file
|
||||
in the compilation folder called ``liblammps.a`` or ``liblammps_<name>.a``
|
||||
in case of building a static library. In case of a shared library
|
||||
|
|
|
|||
|
|
@ -37,7 +37,7 @@ enable (or "install") them first, as discussed on the :doc:`Build
|
|||
package <Build_package>` doc page. If a packages requires (provided or
|
||||
external) libraries, you must configure and build those libraries
|
||||
**before** building LAMMPS itself and especially **before** enabling
|
||||
such a package with ``make yes-<package>``. Building :doc:`LAMMPS with
|
||||
such a package with ``make yes-<package>``. :doc:`Building LAMMPS with
|
||||
CMake <Build_cmake>` can automate much of this for many types of
|
||||
machines, especially workstations, desktops, and laptops, so we suggest
|
||||
you try it first when building LAMMPS in those cases.
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@ explain how to do this for building both with CMake and make.
|
|||
|
||||
* :ref:`C++11 standard compliance <cxx11>` when building all of LAMMPS
|
||||
* :ref:`FFT library <fft>` for use with the :doc:`kspace_style pppm <kspace_style>` command
|
||||
* :ref:`Size of LAMMPS data types <size>`
|
||||
* :ref:`Size of LAMMPS integer types <size>`
|
||||
* :ref:`Read or write compressed files <gzip>`
|
||||
* :ref:`Output of JPG and PNG files <graphics>` via the :doc:`dump image <dump_image>` command
|
||||
* :ref:`Output of movie files <graphics>` via the :doc:`dump_movie <dump_image>` command
|
||||
|
|
@ -123,7 +123,8 @@ per-timestep CPU cost, FFTs are only a portion of long-range
|
|||
Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
|
||||
communication can be costly). A breakdown of these timings is printed
|
||||
to the screen at the end of a run when using the
|
||||
:doc:`kspace_style pppm <kspace_style>` command. The :doc:`Run output <Run_output>`
|
||||
:doc:`kspace_style pppm <kspace_style>` command. The
|
||||
:doc:`Screen and logfile output <Run_output>`
|
||||
doc page gives more details. A more detailed (and time consuming)
|
||||
report of the FFT performance is generated with the
|
||||
:doc:`kspace_modify fftbench yes <kspace_modify>` command.
|
||||
|
|
|
|||
|
|
@ -38,7 +38,7 @@ optional Windows feature allows you to run the bash shell from Ubuntu
|
|||
from within Windows and from there on, you can pretty much use that
|
||||
shell like you are running on an Ubuntu Linux machine (e.g. installing
|
||||
software via apt-get and more). For more details on that, please
|
||||
see :doc:`this tutorial <Howto_wsl>`
|
||||
see :doc:`this tutorial <Howto_wsl>`.
|
||||
|
||||
.. _gnu:
|
||||
|
||||
|
|
|
|||
|
|
@ -17,6 +17,11 @@ ways through the :doc:`compute chunk/atom <compute_chunk_atom>` command
|
|||
and then averaging is done using :doc:`fix ave/chunk <fix_ave_chunk>`.
|
||||
Please refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
|
||||
|
||||
Reset_ids command
|
||||
-----------------
|
||||
|
||||
The reset_ids command has been renamed to :doc:`reset_atom_ids <reset_atom_ids>`.
|
||||
|
||||
MEAM package
|
||||
------------
|
||||
|
||||
|
|
@ -27,7 +32,7 @@ which removes several restrictions (e.g. there can be multiple instances
|
|||
in hybrid pair styles) and allows for some optimizations leading
|
||||
to better performance. The new pair style :doc:`meam/c <pair_meamc>` has
|
||||
the exact same syntax as the old "meam" pair style and thus pair style
|
||||
:doc:`meam <pair_meamc>` is an alias to the new style and backward
|
||||
meam is an alias to the new style and backward
|
||||
compatibility of old inputs is preserved.
|
||||
|
||||
REAX package
|
||||
|
|
|
|||
|
|
@ -6,23 +6,25 @@ the steps outlined below:
|
|||
|
||||
* Check the `New features and bug fixes
|
||||
<https://lammps.sandia.gov/bug.html>`_ section of the `LAMMPS WWW site
|
||||
<lws_>`_ to see if the bug has already been addressed in a patch.
|
||||
<https://lammps.sandia.gov>`_ or the
|
||||
`GitHub Releases page <https://github.com/lammps/lammps/releases>`_ to
|
||||
see if the bug has already been addressed in a patch release.
|
||||
* Check that your issue can be reproduced with the latest development
|
||||
version of LAMMPS.
|
||||
* Check the manual carefully to verify that the unexpected behavior you
|
||||
are observing is indeed in conflict with the documentation
|
||||
* Check the `GitHub Issue page <gip_>`_
|
||||
* Check the `GitHub Issue page <https://github.com/lammps/lammps/issues>`_
|
||||
if your issue has already been reported and if it is still open.
|
||||
* Check the `GitHub Pull Requests page <https://github.com/lammps/pulls>`_
|
||||
if there is already a fix for your bug pending.
|
||||
* Check the `GitHub Pull Requests page <https://github.com/lammps/lammps/pulls>`_
|
||||
to see if there is already a fix for your bug pending.
|
||||
* Check the `mailing list archives <https://lammps.sandia.gov/mail.html>`_
|
||||
to see if the issue has been discussed before.
|
||||
|
||||
If none of these steps yields any useful information, please file a new
|
||||
bug report on the `GitHub Issue page <gip_>`_. The website will offer
|
||||
you to select a suitable template with explanations and then you should
|
||||
replace those explanations with the information that you can provide to
|
||||
reproduce your issue.
|
||||
bug report on the `GitHub Issue page <https://github.com/lammps/lammps/issues>`_.
|
||||
The website will offer you to select a suitable template with explanations
|
||||
and then you should replace those explanations with the information that
|
||||
you can provide to reproduce your issue.
|
||||
|
||||
The most useful thing you can do to help us verify and fix a bug is to
|
||||
isolate the problem. Run it on the smallest number of atoms and fewest
|
||||
|
|
@ -33,7 +35,7 @@ Please avoid using binary restart files unless the issue requires it.
|
|||
In the latter case you should also include an input deck to quickly
|
||||
generate this restart from a data file or a simple additional input.
|
||||
This input deck can be used with tools like a debugger or `valgrind
|
||||
<valgrind_>`_ to further :doc:`debug the crash <Errors_debug>`.
|
||||
<https://valgrind.org>`_ to further :doc:`debug the crash <Errors_debug>`.
|
||||
|
||||
You may also send an email to the LAMMPS mailing list at
|
||||
"lammps-users at lists.sourceforge.net" describing the problem with the
|
||||
|
|
@ -44,6 +46,3 @@ is overlooked and then forgotten. Issues on GitHub have to be explicitly
|
|||
closed, so that will *guarantee* that at least one LAMMPS developer will
|
||||
have looked at it.
|
||||
|
||||
.. _lws: https://lammps.sandia.gov
|
||||
.. _gip: https://github.com/lammps/issues
|
||||
.. _valgrind: https://valgrind.org
|
||||
|
|
|
|||
|
|
@ -48,8 +48,10 @@ to see it on the screen. If you get an error like "Invalid ...
|
|||
style", with ... being fix, compute, pair, etc, it means that you
|
||||
mistyped the style name or that the command is part of an optional
|
||||
package which was not compiled into your executable. The list of
|
||||
available styles in your executable can be listed by using :doc:`the -h command-line swith <Run_options>`. The installation and
|
||||
compilation of optional packages is explained on the :doc:`Build packages <Build_package>` doc page.
|
||||
available styles in your executable can be listed by using
|
||||
:doc:`the -h command-line switch <Run_options>`. The installation and
|
||||
compilation of optional packages is explained on the
|
||||
:doc:`Build packages <Build_package>` doc page.
|
||||
|
||||
For a given command, LAMMPS expects certain arguments in a specified
|
||||
order. If you mess this up, LAMMPS will often flag the error, but it
|
||||
|
|
|
|||
|
|
@ -27,7 +27,7 @@ be quickly post-processed into a movie using commands described on the
|
|||
:doc:`dump image <dump_image>` doc page.
|
||||
|
||||
Animations of many of the examples can be viewed on the Movies section
|
||||
of the `LAMMPS web site <lws_>`_.
|
||||
of the `LAMMPS web site <https://lammps.sandia.gov/movies.html>`_.
|
||||
|
||||
There are two kinds of sub-directories in the examples folder. Lower
|
||||
case named directories contain one or a few simple, quick-to-run
|
||||
|
|
@ -223,4 +223,3 @@ instructions. See the :doc:`Packages_details <Packages_details>` doc
|
|||
page for more info on specific USER packages.
|
||||
|
||||
.. _openkim: https://openkim.org
|
||||
.. _lws: https://lammps.sandia.gov
|
||||
|
|
|
|||
|
|
@ -3,7 +3,7 @@ Howto discussions
|
|||
|
||||
These doc pages describe how to perform various tasks with LAMMPS,
|
||||
both for users and developers. The
|
||||
`glossary <https://lammps.sandia.gov>`_ website page also lists MD
|
||||
`glossary <https://lammps.sandia.gov/glossary.html>`_ website page also lists MD
|
||||
terminology with links to corresponding LAMMPS manual pages. The
|
||||
example input scripts included in the examples directory of the LAMMPS
|
||||
distribution and highlighted on the :doc:`Examples <Examples>` doc page
|
||||
|
|
|
|||
|
|
@ -6,14 +6,14 @@ Use the :doc:`dimension <dimension>` command to specify a 2d simulation.
|
|||
Make the simulation box periodic in z via the :doc:`boundary <boundary>`
|
||||
command. This is the default.
|
||||
|
||||
If using the :doc:`create box <create_box>` command to define a
|
||||
If using the :doc:`create_box <create_box>` command to define a
|
||||
simulation box, set the z dimensions narrow, but finite, so that the
|
||||
create_atoms command will tile the 3d simulation box with a single z
|
||||
plane of atoms - e.g.
|
||||
:doc:`create_atoms <create_atoms>` command will fill the 3d simulation
|
||||
box with a single z plane of atoms - e.g.
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
:doc:`create box <create_box>` 1 -10 10 -10 10 -0.25 0.25
|
||||
create box 1 -10 10 -10 10 -0.25 0.25
|
||||
|
||||
If using the :doc:`read data <read_data>` command to read in a file of
|
||||
atom coordinates, set the "zlo zhi" values to be finite but narrow,
|
||||
|
|
|
|||
|
|
@ -32,9 +32,9 @@ thus how they can be used to compute pairwise body/body or
|
|||
bond/non-body (point particle) interactions. More details of each
|
||||
style are described below.
|
||||
|
||||
More styles may be added in the future. See the :doc:`Modify body
|
||||
<Modify_body>` doc page for details on how to add a new body style to
|
||||
the code.
|
||||
More styles may be added in the future. See the
|
||||
:doc:`page on creating new body styles <Modify_body>` for details on
|
||||
how to add a new body style to the code.
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -198,7 +198,8 @@ explained on the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` co
|
|||
|
||||
(7) An example for using one set of per-chunk values for molecule
|
||||
chunks, to create a second set of micelle-scale chunks (clustered
|
||||
molecules, due to hydrophobicity), is explained on the :doc:`compute chunk/reduce <compute_reduce_chunk>` command doc page.
|
||||
molecules, due to hydrophobicity), is explained on the
|
||||
:doc:`compute reduce/chunk <compute_reduce_chunk>` command doc page.
|
||||
|
||||
(8) An example for using one set of per-chunk values (dipole moment
|
||||
vectors) for molecule chunks, spreading the values to each atom in
|
||||
|
|
|
|||
|
|
@ -29,7 +29,7 @@ molecular systems (:ref:`Lamoureux and Roux <howto-Lamoureux>`):
|
|||
to the total charge of the core atom).
|
||||
|
||||
A detailed tutorial covering the usage of Drude induced dipoles in
|
||||
LAMMPS is on the :doc:`Howto drude2e <Howto_drude2>` doc page.
|
||||
LAMMPS is on the :doc:`here <Howto_drude2>`.
|
||||
|
||||
As with the core-shell model, the cores and Drude particles should
|
||||
appear in the data file as standard atoms. The same holds for the
|
||||
|
|
|
|||
|
|
@ -377,7 +377,7 @@ For our phenol example, the groups would be defined as
|
|||
Note that with the fixes *drude/transform*\ , it is not required to
|
||||
specify *comm_modify vel yes* because the fixes do it anyway (several
|
||||
times and for the forces also). To avoid the flying ice cube artifact
|
||||
:ref:`(Lamoureux) <Lamoureux2>`, where the atoms progressively freeze and the
|
||||
:ref:`(Lamoureux and Roux) <Lamoureux2>`, where the atoms progressively freeze and the
|
||||
center of mass of the whole system drifts faster and faster, the *fix
|
||||
momentum* can be used. For instance:
|
||||
|
||||
|
|
@ -456,7 +456,7 @@ NPT ensemble using Nose-Hoover thermostat:
|
|||
|
||||
.. _Lamoureux2:
|
||||
|
||||
**(Lamoureux)** Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003)
|
||||
**(Lamoureux and Roux)** Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003)
|
||||
|
||||
.. _Schroeder:
|
||||
|
||||
|
|
|
|||
|
|
@ -20,7 +20,7 @@ work required by the LAMMPS developers. Consequently, creating a pull
|
|||
request will increase your chances to have your contribution included
|
||||
and will reduce the time until the integration is complete. For more
|
||||
information on the requirements to have your code included into LAMMPS
|
||||
please see the :doc:`Modify contribute <Modify_contribute>` doc page.
|
||||
please see :doc:`this page <Modify_contribute>`.
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -114,7 +114,7 @@ will only rotate and experience torque if the force field computes
|
|||
such interactions. These are the various :doc:`pair styles <pair_style>` that generate torque:
|
||||
|
||||
* :doc:`pair_style gran/history <pair_gran>`
|
||||
* :doc:`pair_style gran/hertzian <pair_gran>`
|
||||
* :doc:`pair_style gran/hertz <pair_gran>`
|
||||
* :doc:`pair_style gran/no_history <pair_gran>`
|
||||
* :doc:`pair_style dipole/cut <pair_dipole>`
|
||||
* :doc:`pair_style gayberne <pair_gayberne>`
|
||||
|
|
|
|||
|
|
@ -42,12 +42,12 @@ particles.
|
|||
DPD thermostatting alters pairwise interactions in a manner analogous
|
||||
to the per-particle thermostatting of :doc:`fix langevin <fix_langevin>`.
|
||||
|
||||
Any of the thermostatting fixes can use :doc:`temperature computes <Howto_thermostat>` that remove bias which has two
|
||||
effects. First, the current calculated temperature, which is compared
|
||||
to the requested target temperature, is calculated with the velocity
|
||||
bias removed. Second, the thermostat adjusts only the thermal
|
||||
temperature component of the particle's velocities, which are the
|
||||
velocities with the bias removed. The removed bias is then added back
|
||||
Any of the thermostatting fixes can be instructed to use custom temperature
|
||||
computes that remove bias which has two effects: first, the current
|
||||
calculated temperature, which is compared to the requested target temperature,
|
||||
is calculated with the velocity bias removed; second, the thermostat adjusts
|
||||
only the thermal temperature component of the particle's velocities, which are
|
||||
the velocities with the bias removed. The removed bias is then added back
|
||||
to the adjusted velocities. See the doc pages for the individual
|
||||
fixes and for the :doc:`fix_modify <fix_modify>` command for
|
||||
instructions on how to assign a temperature compute to a
|
||||
|
|
@ -55,7 +55,24 @@ thermostatting fix. For example, you can apply a thermostat to only
|
|||
the x and z components of velocity by using it in conjunction with
|
||||
:doc:`compute temp/partial <compute_temp_partial>`. Of you could
|
||||
thermostat only the thermal temperature of a streaming flow of
|
||||
particles without affecting the streaming velocity, by using :doc:`compute temp/profile <compute_temp_profile>`.
|
||||
particles without affecting the streaming velocity, by using
|
||||
:doc:`compute temp/profile <compute_temp_profile>`.
|
||||
|
||||
Below is a list of some custom temperature computes that can be used like that:
|
||||
|
||||
* :doc:`compute_temp_asphere`
|
||||
* :doc:`compute_temp_body`
|
||||
* :doc:`compute_temp_chunk`
|
||||
* :doc:`compute_temp_com`
|
||||
* :doc:`compute_temp_deform`
|
||||
* :doc:`compute_temp_partial`
|
||||
* :doc:`compute_temp_profile`
|
||||
* :doc:`compute_temp_ramp`
|
||||
* :doc:`compute_temp_region`
|
||||
* :doc:`compute_temp_rotate`
|
||||
* :doc:`compute_temp_sphere`
|
||||
|
||||
|
||||
|
||||
.. note::
|
||||
|
||||
|
|
|
|||
|
|
@ -5,8 +5,8 @@ The shear viscosity eta of a fluid can be measured in at least 6 ways
|
|||
using various options in LAMMPS. See the examples/VISCOSITY directory
|
||||
for scripts that implement the 5 methods discussed here for a simple
|
||||
Lennard-Jones fluid model and 1 method for SPC/E water model.
|
||||
Also, see the :doc:`Howto kappa <Howto_kappa>` doc page for an analogous discussion for
|
||||
thermal conductivity.
|
||||
Also, see the :doc:`page on calculating thermal conductivity <Howto_kappa>`
|
||||
for an analogous discussion for thermal conductivity.
|
||||
|
||||
Eta is a measure of the propensity of a fluid to transmit momentum in
|
||||
a direction perpendicular to the direction of velocity or momentum
|
||||
|
|
|
|||
|
|
@ -51,15 +51,14 @@ Or they can be generated from the content provided in doc/src by
|
|||
typing ``make html`` from the doc directory.
|
||||
|
||||
After initial cloning, as bug fixes and new features are added to
|
||||
LAMMPS, as listed on :doc:`this page <Errors_bugs>`, you can stay
|
||||
up-to-date by typing the following git commands from within the
|
||||
"mylammps" directory:
|
||||
LAMMPS you can stay up-to-date by typing the following git commands
|
||||
from within the "mylammps" directory:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
$ git checkout unstable # not needed if you always stay in this branch
|
||||
$ git checkout stable # use one of the 3 checkout commands
|
||||
$ git checkout master
|
||||
$ git checkout stable # use one of these 3 checkout commands
|
||||
$ git checkout master # to choose the branch to follow
|
||||
$ git pull
|
||||
|
||||
Doing a "pull" will not change any files you have added to the LAMMPS
|
||||
|
|
@ -82,8 +81,8 @@ Stable versions and what tagID to use for a particular stable version
|
|||
are discussed on `this page <https://lammps.sandia.gov/bug.html#version>`_.
|
||||
Note that this command will print some warnings, because in order to get
|
||||
back to the latest revision and to be able to update with ``git pull``
|
||||
again, you first will need to first type ``git checkout unstable`` (or
|
||||
check out any other desired branch).
|
||||
again, you will need to do ``git checkout unstable`` (or
|
||||
check out any other desired branch) first.
|
||||
|
||||
Once you have updated your local files with a ``git pull`` (or ``git
|
||||
checkout``), you still need to re-build LAMMPS if any source files have
|
||||
|
|
@ -95,7 +94,7 @@ changed. To do this, you should cd to the src directory and type:
|
|||
$ make package-update # sync package files with src files
|
||||
$ make foo # re-build for your machine (mpi, serial, etc)
|
||||
|
||||
just as described on the :doc:`Install patch <Install_patch>` doc page,
|
||||
just as described on the :doc:`Apply patch <Install_patch>` doc page,
|
||||
after a patch has been installed.
|
||||
|
||||
.. warning::
|
||||
|
|
|
|||
|
|
@ -6,9 +6,12 @@ if you use git to track the LAMMPS development. Instructions for
|
|||
how to stay current are on the
|
||||
:doc:`Download the LAMMPS source with git <Install_git>` page.
|
||||
|
||||
If you prefer to download a tarball, as described on the :doc:`Install git <Install_tarball>` doc page, you can stay current by
|
||||
If you prefer to download a tarball, as described on the
|
||||
:doc:`tarball download <Install_tarball>` page, you can stay current by
|
||||
downloading "patch files" when new patch releases are made. A link to
|
||||
a patch file is posted on the `bug and feature page <https://lammps.sandia.gov/bug.html>`_ of the LAMMPS website, along
|
||||
a patch file is posted on the
|
||||
`bugf fixes and new feature page <https://lammps.sandia.gov/bug.html>`_
|
||||
of the LAMMPS website, along
|
||||
with a list of changed files and details about what is in the new patch
|
||||
release. This page explains how to apply the patch file to your local
|
||||
LAMMPS directory.
|
||||
|
|
|
|||
|
|
@ -181,7 +181,7 @@ Pre- and post-processing
|
|||
|
||||
* A handful of pre- and post-processing tools are packaged with LAMMPS,
|
||||
some of which can convert input and output files to/from formats used
|
||||
by other codes; see the :doc:`Toos <Tools>` doc page.
|
||||
by other codes; see the :doc:`Tools <Tools>` doc page.
|
||||
* Our group has also written and released a separate toolkit called
|
||||
`Pizza.py <pizza_>`_ which provides tools for doing setup, analysis,
|
||||
plotting, and visualization for LAMMPS simulations. Pizza.py is
|
||||
|
|
@ -197,7 +197,7 @@ Specialized features
|
|||
----------------------------------
|
||||
|
||||
LAMMPS can be built with optional packages which implement a variety
|
||||
of additional capabilities. See the :doc:`Packages <Packages>` doc
|
||||
of additional capabilities. See the :doc:`Optional Packages <Packages>`
|
||||
page for details.
|
||||
|
||||
These are LAMMPS capabilities which you may not think of as typical
|
||||
|
|
@ -214,7 +214,7 @@ classical MD options:
|
|||
* Monte Carlo via :doc:`GCMC <fix_gcmc>` and :doc:`tfMC <fix_tfmc>` and :doc:`atom swapping <fix_atom_swap>`
|
||||
* :doc:`path-integral molecular dynamics (PIMD) <fix_ipi>` and :doc:`this as well <fix_pimd>`
|
||||
* :doc:`Direct Simulation Monte Carlo <pair_dsmc>` for low-density fluids
|
||||
* :doc:`Peridynamics mesoscale modeling <pair_peri>`
|
||||
* :doc:`Peridynamics modeling <pair_peri>`
|
||||
* :doc:`Lattice Boltzmann fluid <fix_lb_fluid>`
|
||||
* :doc:`targeted <fix_tmd>` and :doc:`steered <fix_smd>` molecular dynamics
|
||||
* :doc:`two-temperature electron model <fix_ttm>`
|
||||
|
|
|
|||
|
|
@ -66,8 +66,10 @@ Here are suggestions on how to perform these tasks:
|
|||
on-the-fly via its :doc:`dump image <dump_image>` command and pass
|
||||
them to an external program, `FFmpeg <https://www.ffmpeg.org>`_ to generate
|
||||
movies from them. For high-quality, interactive visualization there are
|
||||
many excellent and free tools available. See the `Other Codes page <https://lammps.sandia.gov/viz.html>`_ page of the LAMMPS website for
|
||||
visualization packages that can use LAMMPS output data.
|
||||
many excellent and free tools available. See the
|
||||
`Visualization Tools <https://lammps.sandia.gov/viz.html>`_ page of the
|
||||
LAMMPS website for
|
||||
visualization packages that can process LAMMPS output data.
|
||||
* **Plotting:** See the next bullet about Pizza.py as well as the
|
||||
:doc:`Python <Python_head>` doc page for examples of plotting LAMMPS
|
||||
output. Scripts provided with the *python* tool in the tools
|
||||
|
|
|
|||
|
|
@ -15,7 +15,7 @@ that supports the `MPI <mpi_>`_ message-passing library. This includes
|
|||
shared-memory boxes and distributed-memory clusters and
|
||||
supercomputers.
|
||||
|
||||
.. _mpi: http://www-unix.mcs.anl.gov/mpi
|
||||
.. _mpi: https://en.wikipedia.org/wiki/Message_Passing_Interface
|
||||
.. _lws: https://lammps.sandia.gov
|
||||
|
||||
LAMMPS is written in C++. Earlier versions were written in F77 and
|
||||
|
|
|
|||
|
|
@ -2,22 +2,22 @@ Additional website links
|
|||
========================
|
||||
|
||||
The `LAMMPS website <lws_>`_ has a variety of additional info about
|
||||
LAMMPS, beyond what is in this manual. Some of the other pages in
|
||||
this Intr are included in this list.
|
||||
LAMMPS, beyond what is in this manual. Some other useful resources
|
||||
available online are listed below.
|
||||
|
||||
.. _lws: https://lammps.sandia.gov
|
||||
|
||||
* `Brief intro and recently added significant features <lws_>`_
|
||||
* `List of features <https://lammps.sandia.gov/features.html>`_
|
||||
* `List of non-features <https://lammps.sandia.gov/non_features.html>`_
|
||||
* `List of features <https://lammps.sandia.gov/doc/Intro_features.html>`_
|
||||
* `List of non-features <https://lammps.sandia.gov/doc/Intro_nonfeatures.html>`_
|
||||
* `Recent bug fixes and new features <https://lammps.sandia.gov/bug.html>`_
|
||||
|
||||
* `Download info <https://lammps.sandia.gov/download.html>`_
|
||||
* `GitHub site <https://github.com/lammps/lammps>`_
|
||||
* `SourceForge site <https://sourceforge.net/projects/lammps>`_
|
||||
* `LAMMPS open-source license <https://lammps.sandia.gov/open_source.html>`_
|
||||
* `LAMMPS open-source license <https://lammps.sandia.gov/doc/Intro_opensource.html>`_
|
||||
|
||||
* `Glossary of MD terms relevant to LAMMPS <https://lammps.sandia.gov/glossary.html>`_
|
||||
* `Glossary of terms relevant to LAMMPS <https://lammps.sandia.gov/glossary.html>`_
|
||||
* `LAMMPS highlights with images <https://lammps.sandia.gov/pictures.html>`_
|
||||
* `LAMMPS highlights with movies <https://lammps.sandia.gov/movies.html>`_
|
||||
* `Mail list <https://lammps.sandia.gov/mail.html>`_
|
||||
|
|
|
|||
|
|
@ -27,9 +27,10 @@ all LAMMPS development is coordinated.
|
|||
The content for this manual is part of the LAMMPS distribution. You
|
||||
can build a local copy of the Manual as HTML pages or a PDF file, by
|
||||
following the steps on the :doc:`Manual build <Manual_build>` doc page.
|
||||
The manual is split into two parts:
|
||||
1) :ref:`User documentation <user_documentation>`
|
||||
and 2) :ref:`Programmer documentation <programmer_documentation>`.
|
||||
The manual is organized in two parts:
|
||||
1) A :ref:`User documentation <user_documentation>` for how to install
|
||||
and use LAMMPS and 2) a :ref:`Programmer documentation <programmer_documentation>`
|
||||
for how to write programs using the LAMMPS library or how to modify LAMMPS.
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -8,7 +8,8 @@ this.
|
|||
|
||||
If you add a new feature to LAMMPS and think it will be of interest to
|
||||
general users, we encourage you to submit it for inclusion in LAMMPS
|
||||
as a pull request on our `GitHub site <https://github.com/lammps/lammps>`_, after reading the :doc:`Modify contribute <Modify_contribute>` doc page.
|
||||
as a pull request on our `GitHub site <https://github.com/lammps/lammps>`_,
|
||||
after reading :doc:`this page <Modify_contribute>`.
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
|
|
|
|||
|
|
@ -47,13 +47,13 @@ other strings.
|
|||
* - fields_comm
|
||||
- list of properties communicated to ghost atoms every step
|
||||
* - fields_comm_vel
|
||||
- additional properties communicated if :doc:`comm_modify vel <atom_style>` is used
|
||||
- additional properties communicated if :doc:`comm_modify vel <comm_modify>` is used
|
||||
* - fields_reverse
|
||||
- list of properties summed from ghost atoms every step
|
||||
* - fields_border
|
||||
- list of properties communicated with ghost atoms every reneighboring step
|
||||
* - fields_border_vel
|
||||
- additional properties communicated if :doc:`comm_modify vel <atom_style>` is used
|
||||
- additional properties communicated if :doc:`comm_modify vel <comm_modify>` is used
|
||||
* - fields_exchange
|
||||
- list of properties communicated when an atom migrates to another processor
|
||||
* - fields_restart
|
||||
|
|
|
|||
|
|
@ -31,14 +31,14 @@ send an e-mail to ``slack@lammps.org`` explaining what part of LAMMPS
|
|||
you are working on. Only discussions related to LAMMPS development are
|
||||
tolerated, so this is **NOT** for people that look for help with compiling,
|
||||
installing, or using LAMMPS. Please contact the `lammps-users mailing
|
||||
list <https://lammps.sandia.gov>`_ for those purposes instead.
|
||||
list <https://lammps.sandia.gov/mail.html>`_ for those purposes instead.
|
||||
|
||||
How quickly your contribution will be integrated depends largely on how
|
||||
much effort it will cause to integrate and test it, how much it requires
|
||||
changes to the core codebase, and of how much interest it is to the
|
||||
larger LAMMPS community. Please see below for a checklist of typical
|
||||
requirements. Once you have prepared everything, see the :doc:`Using
|
||||
GitHub with LAMMPS Howto <Howto_github>` doc page for instructions on
|
||||
requirements. Once you have prepared everything, see the :doc:`LAMMPS GitHub
|
||||
Tutorial <Howto_github>` page for instructions on
|
||||
how to submit your changes or new files through a GitHub pull
|
||||
request. If you prefer to submit patches or full files, you should first
|
||||
make certain, that your code works correctly with the latest patch-level
|
||||
|
|
@ -58,8 +58,8 @@ are listed and described on the :doc:`Packages details <Packages_details>` doc p
|
|||
|
||||
Note that by providing us files to release, you are agreeing to make
|
||||
them open-source, i.e. we can release them under the terms of the GPL,
|
||||
used as a license for the rest of LAMMPS. See the `Open source <https://lammps.sandia.gov/open_source.html>`_ page on the LAMMPS
|
||||
website for details.
|
||||
used as a license for the rest of LAMMPS. See the :doc:`LAMMPS license
|
||||
<Intro_opensource>` doc page for details.
|
||||
|
||||
With user packages and files, all we are really providing (aside from
|
||||
the fame and fortune that accompanies having your name in the source
|
||||
|
|
|
|||
|
|
@ -20,7 +20,7 @@ for output. Search for the word "customize" with references to
|
|||
"keyword" in thermo.cpp to see the several locations where code will
|
||||
need to be added.
|
||||
|
||||
Note that the :doc:`thermo_style custom <thermo>` command already allows
|
||||
Note that the :doc:`thermo_style custom <thermo_style>` command already allows
|
||||
for thermo output of quantities calculated by :doc:`fixes <fix>`,
|
||||
:doc:`computes <compute>`, and :doc:`variables <variable>`. Thus, it may
|
||||
be simpler to compute what you wish via one of those constructs, than
|
||||
|
|
|
|||
|
|
@ -299,7 +299,8 @@ Dozens of pair styles and a version of the PPPM long-range Coulombic
|
|||
solver optimized for GPUs. All such styles have a "gpu" as a suffix
|
||||
in their style name. The GPU code can be compiled with either CUDA or
|
||||
OpenCL, however the OpenCL variants are no longer actively maintained
|
||||
and only the CUDA versions are regularly tested. The :doc:`Speed gpu <Speed_gpu>` doc page gives details of what hardware and GPU
|
||||
and only the CUDA versions are regularly tested. The
|
||||
:doc:`Speed_gpu` page gives details of what hardware and GPU
|
||||
software is required on your system, and details on how to build and
|
||||
use this package. Its styles can be invoked at run time via the "-sf
|
||||
gpu" or "-suffix gpu" :doc:`command-line switches <Run_options>`. See
|
||||
|
|
@ -318,8 +319,8 @@ This package has :ref:`specific installation instructions <gpu>` on the :doc:`Bu
|
|||
* src/GPU: filenames -> commands
|
||||
* src/GPU/README
|
||||
* lib/gpu/README
|
||||
* :doc:`Speed packages <Speed_packages>`
|
||||
* :doc:`Speed gpu <Speed_gpu>`
|
||||
* :doc:`Accelerator packages <Speed_packages>`
|
||||
* :doc:`GPU package <Speed_gpu>`
|
||||
* :doc:`Section 2.6 -sf gpu <Run_options>`
|
||||
* :doc:`Section 2.6 -pk gpu <Run_options>`
|
||||
* :doc:`package gpu <package>`
|
||||
|
|
@ -433,7 +434,7 @@ Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute
|
|||
styles adapted to compile using the Kokkos library which can convert
|
||||
them to OpenMP or CUDA code so that they run efficiently on multicore
|
||||
CPUs, KNLs, or GPUs. All the styles have a "kk" as a suffix in their
|
||||
style name. The :doc:`Speed kokkos <Speed_kokkos>` doc page gives
|
||||
style name. The :doc:`KOKKOS package <Speed_kokkos>` doc page gives
|
||||
details of what hardware and software is required on your system, and
|
||||
how to build and use this package. Its styles can be invoked at run
|
||||
time via the "-sf kk" or "-suffix kk" :doc:`command-line switches <Run_options>`. Also see the :ref:`GPU <PKG-GPU>`, :ref:`OPT <PKG-OPT>`,
|
||||
|
|
@ -463,8 +464,8 @@ This package has :ref:`specific installation instructions <kokkos>` on the :doc:
|
|||
* src/KOKKOS: filenames -> commands
|
||||
* src/KOKKOS/README
|
||||
* lib/kokkos/README
|
||||
* :doc:`Speed packages <Speed_packages>`
|
||||
* :doc:`Speed kokkos <Speed_kokkos>`
|
||||
* :doc:`Accelerator packages <Speed_packages>`
|
||||
* :doc:`KOKKOS package <Speed_kokkos>`
|
||||
* :doc:`Section 2.6 -k on ... <Run_options>`
|
||||
* :doc:`Section 2.6 -sf kk <Run_options>`
|
||||
* :doc:`Section 2.6 -pk kokkos <Run_options>`
|
||||
|
|
@ -665,7 +666,7 @@ A general interface for machine-learning interatomic potentials.
|
|||
|
||||
**Install:**
|
||||
|
||||
To use this package, also the :ref:`SNAP package<PKG-SNAP>` needs to be installed.
|
||||
To use this package, also the :ref:`SNAP package <PKG-SNAP>` needs to be installed.
|
||||
|
||||
**Author:** Aidan Thompson (Sandia).
|
||||
|
||||
|
|
@ -773,7 +774,7 @@ OPT package
|
|||
A handful of pair styles which are optimized for improved CPU
|
||||
performance on single or multiple cores. These include EAM, LJ,
|
||||
CHARMM, and Morse potentials. The styles have an "opt" suffix in
|
||||
their style name. The :doc:`Speed opt <Speed_opt>` doc page gives
|
||||
their style name. The :doc:`OPT package <Speed_opt>` doc page gives
|
||||
details of how to build and use this package. Its styles can be
|
||||
invoked at run time via the "-sf opt" or "-suffix opt" :doc:`command-line switches <Run_options>`. See also the :ref:`KOKKOS <PKG-KOKKOS>`,
|
||||
:ref:`USER-INTEL <PKG-USER-INTEL>`, and :ref:`USER-OMP <PKG-USER-OMP>` packages, which
|
||||
|
|
@ -789,8 +790,8 @@ This package has :ref:`specific installation instructions <opt>` on the :doc:`Bu
|
|||
**Supporting info:**
|
||||
|
||||
* src/OPT: filenames -> commands
|
||||
* :doc:`Speed packages <Speed_packages>`
|
||||
* :doc:`Speed opt <Speed_opt>`
|
||||
* :doc:`Accelerator packages <Speed_packages>`
|
||||
* :doc:`OPT package <Speed_opt>`
|
||||
* :doc:`Section 2.6 -sf opt <Run_options>`
|
||||
* Search the :doc:`pair style <Commands_pair>` page for styles followed by (t)
|
||||
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
|
||||
|
|
@ -1541,7 +1542,8 @@ USER-INTEL package
|
|||
|
||||
Dozens of pair, fix, bond, angle, dihedral, improper, and kspace
|
||||
styles which are optimized for Intel CPUs and KNLs (Knights Landing).
|
||||
All of them have an "intel" in their style name. The :doc:`Speed intel <Speed_intel>` doc page gives details of what hardware and
|
||||
All of them have an "intel" in their style name. The
|
||||
:doc:`USER-INTEL package <Speed_intel>` page gives details of what hardware and
|
||||
compilers are required on your system, and how to build and use this
|
||||
package. Its styles can be invoked at run time via the "-sf intel" or
|
||||
"-suffix intel" :doc:`command-line switches <Run_options>`. Also see
|
||||
|
|
@ -1567,8 +1569,8 @@ This package has :ref:`specific installation instructions <user-intel>` on the :
|
|||
|
||||
* src/USER-INTEL: filenames -> commands
|
||||
* src/USER-INTEL/README
|
||||
* :doc:`Speed packages <Speed_packages>`
|
||||
* :doc:`Speed intel <Speed_intel>`
|
||||
* :doc:`Accelerator packages <Speed_packages>`
|
||||
* :doc:`USER-INTEL package <Speed_intel>`
|
||||
* :doc:`Section 2.6 -sf intel <Run_options>`
|
||||
* :doc:`Section 2.6 -pk intel <Run_options>`
|
||||
* :doc:`package intel <package>`
|
||||
|
|
@ -1915,7 +1917,7 @@ USER-OMP package
|
|||
Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and
|
||||
kspace styles which are altered to enable threading on many-core CPUs
|
||||
via OpenMP directives. All of them have an "omp" in their style name.
|
||||
The :doc:`Speed omp <Speed_omp>` doc page gives details of what hardware
|
||||
The :doc:`USER-OMP package <Speed_omp>` page gives details of what hardware
|
||||
and compilers are required on your system, and how to build and use
|
||||
this package. Its styles can be invoked at run time via the "-sf omp"
|
||||
or "-suffix omp" :doc:`command-line switches <Run_options>`. Also see
|
||||
|
|
@ -1947,8 +1949,8 @@ This package has :ref:`specific installation instructions <user-omp>` on the :do
|
|||
|
||||
* src/USER-OMP: filenames -> commands
|
||||
* src/USER-OMP/README
|
||||
* :doc:`Speed packages <Speed_packages>`
|
||||
* :doc:`Speed omp <Speed_omp>`
|
||||
* :doc:`Accelerator packages <Speed_packages>`
|
||||
* :doc:`USER-OMP package <Speed_omp>`
|
||||
* :doc:`Section 2.6 -sf omp <Run_options>`
|
||||
* :doc:`Section 2.6 -pk omp <Run_options>`
|
||||
* :doc:`package omp <package>`
|
||||
|
|
|
|||
|
|
@ -37,7 +37,7 @@ package:
|
|||
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
|
||||
| :ref:`CORESHELL <PKG-CORESHELL>` | adiabatic core/shell model | :doc:`Howto coreshell <Howto_coreshell>` | coreshell | no |
|
||||
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
|
||||
| :ref:`DIPOLE <PKG-DIPOLE>` | point dipole particles | :doc:`pair_style dipole/cut <pair_dipole>` | dipole | no |
|
||||
| :ref:`DIPOLE <PKG-DIPOLE>` | point dipole particles | :doc:`pair_style lj/.../dipole <pair_dipole>` | dipole | no |
|
||||
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
|
||||
| :ref:`GPU <PKG-GPU>` | GPU-enabled styles | :doc:`Section gpu <Speed_gpu>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | int |
|
||||
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
|
||||
|
|
|
|||
|
|
@ -27,11 +27,11 @@ executable itself can be placed elsewhere.
|
|||
|
||||
As LAMMPS runs it prints info to the screen and a logfile named
|
||||
*log.lammps*\ . More info about output is given on the
|
||||
:doc:`Run output <Run_output>` doc page.
|
||||
:doc:`screen and logfile output <Run_output>` page.
|
||||
|
||||
If LAMMPS encounters errors in the input script or while running a
|
||||
simulation it will print an ERROR message and stop or a WARNING
|
||||
message and continue. See the :doc:`Errors <Errors>` doc page for a
|
||||
message and continue. See the :doc:`Common Problems <Errors>` page for a
|
||||
discussion of the various kinds of errors LAMMPS can or can't detect,
|
||||
a list of all ERROR and WARNING messages, and what to do about them.
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@ stdin.
|
|||
|
||||
Explicitly enable or disable KOKKOS support, as provided by the KOKKOS
|
||||
package. Even if LAMMPS is built with this package, as described
|
||||
in :doc:`Speed kokkos <Speed_kokkos>`, this switch must be set to enable
|
||||
in the :doc:`the KOKKOS package page <Speed_kokkos>`, this switch must be set to enable
|
||||
running with KOKKOS-enabled styles the package provides. If the
|
||||
switch is not set (the default), LAMMPS will operate as if the KOKKOS
|
||||
package were not installed; i.e. you can run standard LAMMPS or with
|
||||
|
|
@ -98,7 +98,8 @@ Either the full word or an abbreviation can be used for the keywords.
|
|||
Note that the keywords do not use a leading minus sign. I.e. the
|
||||
keyword is "t", not "-t". Also note that each of the keywords has a
|
||||
default setting. Examples of when to use these options and what
|
||||
settings to use on different platforms is given on the :doc:`Speed kokkos <Speed_kokkos>` doc page.
|
||||
settings to use on different platforms is given on the :doc:`KOKKOS package <Speed_kokkos>`
|
||||
doc page.
|
||||
|
||||
* d or device
|
||||
* g or gpus
|
||||
|
|
@ -268,7 +269,7 @@ machine (e.g. your desktop), you can run on more (virtual) processors
|
|||
than you have physical processors.
|
||||
|
||||
To run multiple independent simulations from one input script, using
|
||||
multiple partitions, see the :doc:`Howto multiple <Howto_multiple>` doc
|
||||
multiple partitions, see the :doc:`Howto multiple <Howto_multiple>`
|
||||
page. World- and universe-style :doc:`variables <variable>` are useful
|
||||
in this context.
|
||||
|
||||
|
|
@ -326,7 +327,7 @@ cores within each node are ranked in a desired order. Or when using
|
|||
the :doc:`run_style verlet/split <run_style>` command with 2 partitions
|
||||
to insure that a specific Kspace processor (in the second partition) is
|
||||
matched up with a specific set of processors in the first partition.
|
||||
See the :doc:`Speed tips <Speed_tips>` doc page for more details.
|
||||
See the :doc:`General tips <Speed_tips>` page for more details.
|
||||
|
||||
If the keyword *nth* is used with a setting *N*\ , then it means every
|
||||
Nth processor will be moved to the end of the ranking. This is useful
|
||||
|
|
@ -385,7 +386,7 @@ implementations, either by environment variables that specify how to
|
|||
order physical processors, or by config files that specify what
|
||||
physical processors to assign to each MPI rank. The -reorder switch
|
||||
simply gives you a portable way to do this without relying on MPI
|
||||
itself. See the :doc:`processors out <processors>` command for how
|
||||
itself. See the :doc:`processors file <processors>` command for how
|
||||
to output info on the final assignment of physical processors to
|
||||
the LAMMPS simulation domain.
|
||||
|
||||
|
|
@ -523,10 +524,10 @@ lj/cut/intel, lj/cut/kk, lj/cut/omp, and lj/cut/opt. A variant style
|
|||
can be specified explicitly in your input script, e.g. pair_style
|
||||
lj/cut/gpu. If the -suffix switch is used the specified suffix
|
||||
(gpu,intel,kk,omp,opt) is automatically appended whenever your input
|
||||
script command creates a new :doc:`atom <atom_style>`,
|
||||
:doc:`pair <pair_style>`, :doc:`fix <fix>`, :doc:`compute <compute>`, or
|
||||
:doc:`run <run_style>` style. If the variant version does not exist,
|
||||
the standard version is created.
|
||||
script command creates a new :doc:`atom style <atom_style>`,
|
||||
:doc:`pair style <pair_style>`, :doc:`fix <fix>`,
|
||||
:doc:`compute <compute>`, or :doc:`run style <run_style>`. If the
|
||||
variant version does not exist, the standard version is created.
|
||||
|
||||
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
|
||||
|
|
@ -579,8 +580,8 @@ index variable in the input script, since index variables cannot be
|
|||
re-defined.
|
||||
|
||||
See the :doc:`variable <variable>` command for more info on defining
|
||||
index and other kinds of variables and the :doc:`Commands parse <Commands_parse>` page for more info on using variables in
|
||||
input scripts.
|
||||
index and other kinds of variables and the :doc:`Parsing rules <Commands_parse>`
|
||||
page for more info on using variables in input scripts.
|
||||
|
||||
.. note::
|
||||
|
||||
|
|
|
|||
|
|
@ -38,7 +38,7 @@ 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
|
||||
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
|
||||
:doc:`Speed packages <Speed_packages>` doc 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.
|
||||
|
||||
The bench/POTENTIALS directory has input files which correspond to the
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@ different back end languages such as CUDA, OpenMP, or Pthreads. The
|
|||
Kokkos library also provides data abstractions to adjust (at compile
|
||||
time) the memory layout of data structures like 2d and 3d arrays to
|
||||
optimize performance on different hardware. For more information on
|
||||
Kokkos, see `GitHub <https://github.com/kokkos/kokkos>`_.
|
||||
Kokkos, see `the Kokkos GitHub page <https://github.com/kokkos/kokkos>`_.
|
||||
|
||||
The LAMMPS KOKKOS package contains versions of pair, fix, and atom
|
||||
styles that use data structures and macros provided by the Kokkos
|
||||
|
|
@ -20,20 +20,20 @@ including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez
|
|||
(Sandia). For more information on developing using Kokkos abstractions
|
||||
see the Kokkos `Wiki <https://github.com/kokkos/kokkos/wiki>`_.
|
||||
|
||||
Kokkos currently provides support for 3 modes of execution (per MPI
|
||||
Kokkos currently provides support for 4 modes of execution (per MPI
|
||||
task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
|
||||
(threading for many-core CPUs and Intel Phi), and CUDA (for NVIDIA
|
||||
GPUs). You choose the mode at build time to produce an executable
|
||||
compatible with specific hardware.
|
||||
(threading for many-core CPUs and Intel Phi), CUDA (for NVIDIA
|
||||
GPUs) and HIP (for AMD GPUs). You choose the mode at build time to
|
||||
produce an executable compatible with a specific hardware.
|
||||
|
||||
.. note::
|
||||
.. admonition:: NVIDIA CUDA support
|
||||
|
||||
To build with Kokkos support for NVIDIA GPUs, the NVIDIA CUDA toolkit
|
||||
software version 9.0 or later must be installed on your system. See
|
||||
the discussion for the :doc:`GPU package <Speed_gpu>` for details of
|
||||
how to check and do this.
|
||||
|
||||
.. note::
|
||||
.. admonition:: CUDA and MPI library compatibility
|
||||
|
||||
Kokkos with CUDA currently implicitly assumes that the MPI library is
|
||||
CUDA-aware. This is not always the case, especially when using
|
||||
|
|
@ -45,6 +45,13 @@ compatible with specific hardware.
|
|||
LAMMPS command line or by using the command :doc:`package kokkos
|
||||
cuda/aware off <package>` in the input file.
|
||||
|
||||
.. admonition:: AMD GPU support
|
||||
|
||||
To build with Kokkos the HIPCC compiler from the AMD ROCm software
|
||||
version 3.5 or later is required. Supporting this Kokkos mode in
|
||||
LAMMPS is still work in progress. Please contact the LAMMPS developers
|
||||
if you run into problems.
|
||||
|
||||
Building LAMMPS with the KOKKOS package
|
||||
"""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
|
|
|
|||
|
|
@ -14,7 +14,7 @@ timings; you can simply extrapolate from short runs.
|
|||
|
||||
For the set of runs, look at the timing data printed to the screen and
|
||||
log file at the end of each LAMMPS run. The
|
||||
:doc:`Run_output <Run_output>` doc page gives an overview.
|
||||
:doc:`screen and logfile output <Run_output>` page gives an overview.
|
||||
|
||||
Running on one (or a few processors) should give a good estimate of
|
||||
the serial performance and what portions of the timestep are taking
|
||||
|
|
|
|||
|
|
@ -86,7 +86,8 @@ USER-OMP style (in serial or parallel) with a single thread per MPI
|
|||
task, versus running standard LAMMPS with its standard un-accelerated
|
||||
styles (in serial or all-MPI parallelization with 1 task/core). This
|
||||
is because many of the USER-OMP styles contain similar optimizations
|
||||
to those used in the OPT package, described in :doc:`Section 5.3.5 <Speed_opt>`.
|
||||
to those used in the OPT package, described in
|
||||
:doc:`the OPT package <Speed_opt>` doc page.
|
||||
|
||||
With multiple threads/task, the optimal choice of number of MPI
|
||||
tasks/node and OpenMP threads/task can vary a lot and should always be
|
||||
|
|
@ -95,7 +96,8 @@ specific machine, paying attention to guidelines discussed in the next
|
|||
sub-section.
|
||||
|
||||
A description of the multi-threading strategy used in the USER-OMP
|
||||
package and some performance examples are `presented here <http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1>`_
|
||||
package and some performance examples are
|
||||
`presented here <http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1>`_.
|
||||
|
||||
Guidelines for best performance
|
||||
"""""""""""""""""""""""""""""""
|
||||
|
|
|
|||
|
|
@ -1,16 +1,12 @@
|
|||
.. index:: angle_style charmm
|
||||
.. index:: angle_style charmm/intel
|
||||
.. index:: angle_style charmm/kk
|
||||
.. index:: angle_style charmm/omp
|
||||
|
||||
angle_style charmm command
|
||||
==========================
|
||||
|
||||
angle_style charmm/intel command
|
||||
================================
|
||||
|
||||
angle_style charmm/kk command
|
||||
=============================
|
||||
|
||||
angle_style charmm/omp command
|
||||
==============================
|
||||
Accelerator Variants: *charmm/intel*, *charmm/kk*, *charmm/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,13 +1,12 @@
|
|||
.. index:: angle_style class2
|
||||
.. index:: angle_style class2/kk
|
||||
.. index:: angle_style class2/omp
|
||||
.. index:: angle_style class2/p6
|
||||
|
||||
angle_style class2 command
|
||||
==========================
|
||||
|
||||
angle_style class2/kk command
|
||||
=============================
|
||||
|
||||
angle_style class2/omp command
|
||||
==============================
|
||||
Accelerator Variants: *class2/kk*, *class2/omp*
|
||||
|
||||
angle_style class2/p6 command
|
||||
=============================
|
||||
|
|
|
|||
|
|
@ -1,13 +1,11 @@
|
|||
.. index:: angle_style cosine
|
||||
.. index:: angle_style cosine/omp
|
||||
.. index:: angle_style cosine/kk
|
||||
|
||||
angle_style cosine command
|
||||
==========================
|
||||
|
||||
angle_style cosine/omp command
|
||||
==============================
|
||||
|
||||
angle_style cosine/kk command
|
||||
=============================
|
||||
Accelerator Variants: *cosine/omp*, *cosine/kk*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: angle_style cosine/delta
|
||||
.. index:: angle_style cosine/delta/omp
|
||||
|
||||
angle_style cosine/delta command
|
||||
================================
|
||||
|
||||
angle_style cosine/delta/omp command
|
||||
====================================
|
||||
Accelerator Variants: *cosine/delta/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: angle_style cosine/periodic
|
||||
.. index:: angle_style cosine/periodic/omp
|
||||
|
||||
angle_style cosine/periodic command
|
||||
===================================
|
||||
|
||||
angle_style cosine/periodic/omp command
|
||||
=======================================
|
||||
Accelerator Variants: *cosine/periodic/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: angle_style cosine/shift
|
||||
.. index:: angle_style cosine/shift/omp
|
||||
|
||||
angle_style cosine/shift command
|
||||
=================================
|
||||
================================
|
||||
|
||||
angle_style cosine/shift/omp command
|
||||
====================================
|
||||
Accelerator Variants: *cosine/shift/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: angle_style cosine/shift/exp
|
||||
.. index:: angle_style cosine/shift/exp/omp
|
||||
|
||||
angle_style cosine/shift/exp command
|
||||
====================================
|
||||
|
||||
angle_style cosine/shift/exp/omp command
|
||||
========================================
|
||||
Accelerator Variants: *cosine/shift/exp/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: angle_style cosine/squared
|
||||
.. index:: angle_style cosine/squared/omp
|
||||
|
||||
angle_style cosine/squared command
|
||||
==================================
|
||||
|
||||
angle_style cosine/squared/omp command
|
||||
======================================
|
||||
Accelerator Variants: *cosine/squared/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
.. index:: angle_style cross
|
||||
|
||||
angle_style cross command
|
||||
==========================
|
||||
=========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: angle_style dipole
|
||||
.. index:: angle_style dipole/omp
|
||||
|
||||
angle_style dipole command
|
||||
==========================
|
||||
|
||||
angle_style dipole/omp command
|
||||
==============================
|
||||
Accelerator Variants: *dipole/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: angle_style fourier
|
||||
.. index:: angle_style fourier/omp
|
||||
|
||||
angle_style fourier command
|
||||
===========================
|
||||
|
||||
angle_style fourier/omp command
|
||||
===============================
|
||||
Accelerator Variants: *fourier/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: angle_style fourier/simple
|
||||
.. index:: angle_style fourier/simple/omp
|
||||
|
||||
angle_style fourier/simple command
|
||||
==================================
|
||||
|
||||
angle_style fourier/simple/omp command
|
||||
======================================
|
||||
Accelerator Variants: *fourier/simple/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,16 +1,12 @@
|
|||
.. index:: angle_style harmonic
|
||||
.. index:: angle_style harmonic/intel
|
||||
.. index:: angle_style harmonic/kk
|
||||
.. index:: angle_style harmonic/omp
|
||||
|
||||
angle_style harmonic command
|
||||
============================
|
||||
|
||||
angle_style harmonic/intel command
|
||||
==================================
|
||||
|
||||
angle_style harmonic/kk command
|
||||
===============================
|
||||
|
||||
angle_style harmonic/omp command
|
||||
================================
|
||||
Accelerator Variants: *harmonic/intel*, *harmonic/kk*, *harmonic/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: angle_style quartic
|
||||
.. index:: angle_style quartic/omp
|
||||
|
||||
angle_style quartic command
|
||||
===========================
|
||||
|
||||
angle_style quartic/omp command
|
||||
===============================
|
||||
Accelerator Variants: *quartic/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: angle_style sdk
|
||||
.. index:: angle_style sdk/omp
|
||||
|
||||
angle_style sdk command
|
||||
=======================
|
||||
|
||||
angle_style sdk/omp command
|
||||
===========================
|
||||
Accelerator Variants: *sdk/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: angle_style table
|
||||
.. index:: angle_style table/omp
|
||||
|
||||
angle_style table command
|
||||
=========================
|
||||
|
||||
angle_style table/omp command
|
||||
=============================
|
||||
Accelerator Variants: *table/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,13 +1,11 @@
|
|||
.. index:: bond_style class2
|
||||
.. index:: bond_style class2/omp
|
||||
.. index:: bond_style class2/kk
|
||||
|
||||
bond_style class2 command
|
||||
=========================
|
||||
|
||||
bond_style class2/omp command
|
||||
=============================
|
||||
|
||||
bond_style class2/kk command
|
||||
============================
|
||||
Accelerator Variants: *class2/omp*, *class2/kk*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,16 +1,12 @@
|
|||
.. index:: bond_style fene
|
||||
.. index:: bond_style fene/intel
|
||||
.. index:: bond_style fene/kk
|
||||
.. index:: bond_style fene/omp
|
||||
|
||||
bond_style fene command
|
||||
=======================
|
||||
|
||||
bond_style fene/intel command
|
||||
=============================
|
||||
|
||||
bond_style fene/kk command
|
||||
==========================
|
||||
|
||||
bond_style fene/omp command
|
||||
===========================
|
||||
Accelerator Variants: *fene/intel*, *fene/kk*, *fene/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: bond_style fene/expand
|
||||
.. index:: bond_style fene/expand/omp
|
||||
|
||||
bond_style fene/expand command
|
||||
==============================
|
||||
|
||||
bond_style fene/expand/omp command
|
||||
==================================
|
||||
Accelerator Variants: *fene/expand/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: bond_style gromos
|
||||
.. index:: bond_style gromos/omp
|
||||
|
||||
bond_style gromos command
|
||||
=========================
|
||||
|
||||
bond_style gromos/omp command
|
||||
=============================
|
||||
Accelerator Variants: *gromos/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,16 +1,12 @@
|
|||
.. index:: bond_style harmonic
|
||||
.. index:: bond_style harmonic/intel
|
||||
.. index:: bond_style harmonic/kk
|
||||
.. index:: bond_style harmonic/omp
|
||||
|
||||
bond_style harmonic command
|
||||
===========================
|
||||
|
||||
bond_style harmonic/intel command
|
||||
=================================
|
||||
|
||||
bond_style harmonic/kk command
|
||||
==============================
|
||||
|
||||
bond_style harmonic/omp command
|
||||
===============================
|
||||
Accelerator Variants: *harmonic/intel*, *harmonic/kk*, *harmonic/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: bond_style harmonic/shift
|
||||
.. index:: bond_style harmonic/shift/omp
|
||||
|
||||
bond_style harmonic/shift command
|
||||
=================================
|
||||
|
||||
bond_style harmonic/shift/omp command
|
||||
=====================================
|
||||
Accelerator Variants: *harmonic/shift/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: bond_style harmonic/shift/cut
|
||||
.. index:: bond_style harmonic/shift/cut/omp
|
||||
|
||||
bond_style harmonic/shift/cut command
|
||||
=====================================
|
||||
|
||||
bond_style harmonic/shift/cut/omp command
|
||||
=========================================
|
||||
Accelerator Variants: *harmonic/shift/cut/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: bond_style morse
|
||||
.. index:: bond_style morse/omp
|
||||
|
||||
bond_style morse command
|
||||
========================
|
||||
|
||||
bond_style morse/omp command
|
||||
============================
|
||||
Accelerator Variants: *morse/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: bond_style nonlinear
|
||||
.. index:: bond_style nonlinear/omp
|
||||
|
||||
bond_style nonlinear command
|
||||
============================
|
||||
|
||||
bond_style nonlinear/omp command
|
||||
================================
|
||||
Accelerator Variants: *nonlinear/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,4 +1,6 @@
|
|||
.. index:: bond_style oxdna/fene
|
||||
.. index:: bond_style oxdna2/fene
|
||||
.. index:: bond_style oxrna2/fene
|
||||
|
||||
bond_style oxdna/fene command
|
||||
=============================
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: bond_style quartic
|
||||
.. index:: bond_style quartic/omp
|
||||
|
||||
bond_style quartic command
|
||||
==========================
|
||||
|
||||
bond_style quartic/omp command
|
||||
==============================
|
||||
Accelerator Variants: *quartic/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
.. index:: bond_style special
|
||||
|
||||
bond_style special command
|
||||
=================================
|
||||
==========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: bond_style table
|
||||
.. index:: bond_style table/omp
|
||||
|
||||
bond_style table command
|
||||
========================
|
||||
|
||||
bond_style table/omp command
|
||||
============================
|
||||
Accelerator Variants: *table/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,4 +1,6 @@
|
|||
.. index:: compute cluster/atom
|
||||
.. index:: compute fragment/atom
|
||||
.. index:: compute aggregate/atom
|
||||
|
||||
compute cluster/atom command
|
||||
============================
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: compute coord/atom
|
||||
.. index:: compute coord/atom/kk
|
||||
|
||||
compute coord/atom command
|
||||
==========================
|
||||
|
||||
compute coord/atom/kk command
|
||||
===================================
|
||||
Accelerator Variants: *coord/atom/kk*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
.. index:: compute mesont
|
||||
|
||||
compute mesont command
|
||||
==========================
|
||||
======================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: compute orientorder/atom
|
||||
.. index:: compute orientorder/atom/kk
|
||||
|
||||
compute orientorder/atom command
|
||||
================================
|
||||
|
||||
compute orientorder/atom/kk command
|
||||
===================================
|
||||
Accelerator Variants: *orientorder/atom/kk*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,4 +1,5 @@
|
|||
.. index:: compute reduce
|
||||
.. index:: compute reduce/region
|
||||
|
||||
compute reduce command
|
||||
======================
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
.. index:: compute smd/ulsph/effm
|
||||
|
||||
compute smd/ulsph/effm command
|
||||
================================
|
||||
==============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,4 +1,7 @@
|
|||
.. index:: compute sna/atom
|
||||
.. index:: compute snad/atom
|
||||
.. index:: compute snav/atom
|
||||
.. index:: compute snap
|
||||
|
||||
compute sna/atom command
|
||||
========================
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
.. index:: compute sph/e/atom
|
||||
|
||||
compute sph/e/atom command
|
||||
===========================
|
||||
==========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
.. index:: compute sph/rho/atom
|
||||
|
||||
compute sph/rho/atom command
|
||||
=============================
|
||||
============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
.. index:: compute sph/t/atom
|
||||
|
||||
compute sph/t/atom command
|
||||
===========================
|
||||
==========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,4 +1,5 @@
|
|||
.. index:: compute stress/atom
|
||||
.. index:: compute centroid/stress/atom
|
||||
|
||||
compute stress/atom command
|
||||
===========================
|
||||
|
|
|
|||
|
|
@ -1,4 +1,5 @@
|
|||
.. index:: compute stress/mop
|
||||
.. index:: compute stress/mop/profile
|
||||
|
||||
compute stress/mop command
|
||||
==========================
|
||||
|
|
|
|||
|
|
@ -1,4 +1,8 @@
|
|||
.. index:: compute force/tally
|
||||
.. index:: compute heat/flux/tally
|
||||
.. index:: compute pe/tally
|
||||
.. index:: compute pe/mol/tally
|
||||
.. index:: compute stress/tally
|
||||
|
||||
compute force/tally command
|
||||
===========================
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: compute temp
|
||||
.. index:: compute temp/kk
|
||||
|
||||
compute temp command
|
||||
====================
|
||||
|
||||
compute temp/kk command
|
||||
=======================
|
||||
Accelerator Variants: *temp/kk*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,16 +1,13 @@
|
|||
.. index:: dihedral_style charmm
|
||||
.. index:: dihedral_style charmm/intel
|
||||
.. index:: dihedral_style charmm/kk
|
||||
.. index:: dihedral_style charmm/omp
|
||||
.. index:: dihedral_style charmmfsw
|
||||
|
||||
dihedral_style charmm command
|
||||
=============================
|
||||
|
||||
dihedral_style charmm/intel command
|
||||
===================================
|
||||
|
||||
dihedral_style charmm/kk command
|
||||
================================
|
||||
|
||||
dihedral_style charmm/omp command
|
||||
=================================
|
||||
Accelerator Variants: *charmm/intel*, *charmm/kk*, *charmm/omp*
|
||||
|
||||
dihedral_style charmmfsw command
|
||||
================================
|
||||
|
|
|
|||
|
|
@ -1,13 +1,11 @@
|
|||
.. index:: dihedral_style class2
|
||||
.. index:: dihedral_style class2/omp
|
||||
.. index:: dihedral_style class2/kk
|
||||
|
||||
dihedral_style class2 command
|
||||
=============================
|
||||
|
||||
dihedral_style class2/omp command
|
||||
=================================
|
||||
|
||||
dihedral_style class2/kk command
|
||||
================================
|
||||
Accelerator Variants: *class2/omp*, *class2/kk*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: dihedral_style cosine/shift/exp
|
||||
.. index:: dihedral_style cosine/shift/exp/omp
|
||||
|
||||
dihedral_style cosine/shift/exp command
|
||||
=======================================
|
||||
|
||||
dihedral_style cosine/shift/exp/omp command
|
||||
===========================================
|
||||
Accelerator Variants: *cosine/shift/exp/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,13 +1,11 @@
|
|||
.. index:: dihedral_style fourier
|
||||
.. index:: dihedral_style fourier/intel
|
||||
.. index:: dihedral_style fourier/omp
|
||||
|
||||
dihedral_style fourier command
|
||||
==============================
|
||||
|
||||
dihedral_style fourier/intel command
|
||||
====================================
|
||||
|
||||
dihedral_style fourier/omp command
|
||||
==================================
|
||||
Accelerator Variants: *fourier/intel*, *fourier/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,16 +1,12 @@
|
|||
.. index:: dihedral_style harmonic
|
||||
.. index:: dihedral_style harmonic/intel
|
||||
.. index:: dihedral_style harmonic/kk
|
||||
.. index:: dihedral_style harmonic/omp
|
||||
|
||||
dihedral_style harmonic command
|
||||
===============================
|
||||
|
||||
dihedral_style harmonic/intel command
|
||||
=====================================
|
||||
|
||||
dihedral_style harmonic/kk command
|
||||
==================================
|
||||
|
||||
dihedral_style harmonic/omp command
|
||||
===================================
|
||||
Accelerator Variants: *harmonic/intel*, *harmonic/kk*, *harmonic/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: dihedral_style helix
|
||||
.. index:: dihedral_style helix/omp
|
||||
|
||||
dihedral_style helix command
|
||||
============================
|
||||
|
||||
dihedral_style helix/omp command
|
||||
================================
|
||||
Accelerator Variants: *helix/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: dihedral_style multi/harmonic
|
||||
.. index:: dihedral_style multi/harmonic/omp
|
||||
|
||||
dihedral_style multi/harmonic command
|
||||
=====================================
|
||||
|
||||
dihedral_style multi/harmonic/omp command
|
||||
=========================================
|
||||
Accelerator Variants: *multi/harmonic/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: dihedral_style nharmonic
|
||||
.. index:: dihedral_style nharmonic/omp
|
||||
|
||||
dihedral_style nharmonic command
|
||||
=================================
|
||||
================================
|
||||
|
||||
dihedral_style nharmonic/omp command
|
||||
=====================================
|
||||
Accelerator Variants: *nharmonic/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,16 +1,12 @@
|
|||
.. index:: dihedral_style opls
|
||||
.. index:: dihedral_style opls/intel
|
||||
.. index:: dihedral_style opls/kk
|
||||
.. index:: dihedral_style opls/omp
|
||||
|
||||
dihedral_style opls command
|
||||
===========================
|
||||
|
||||
dihedral_style opls/intel command
|
||||
=================================
|
||||
|
||||
dihedral_style opls/kk command
|
||||
==============================
|
||||
|
||||
dihedral_style opls/omp command
|
||||
===============================
|
||||
Accelerator Variants: *opls/intel*, *opls/kk*, *opls/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: dihedral_style quadratic
|
||||
.. index:: dihedral_style quadratic/omp
|
||||
|
||||
dihedral_style quadratic command
|
||||
================================
|
||||
|
||||
dihedral_style quadratic/omp command
|
||||
====================================
|
||||
Accelerator Variants: *quadratic/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
.. index:: dihedral_style table
|
||||
.. index:: dihedral_style table/omp
|
||||
|
||||
dihedral_style table command
|
||||
============================
|
||||
|
||||
dihedral_style table/omp command
|
||||
================================
|
||||
Accelerator Variants: *table/omp*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
.. index:: dihedral_style zero
|
||||
|
||||
dihedral_style zero command
|
||||
============================
|
||||
===========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
|
|
|||
|
|
@ -1,4 +1,5 @@
|
|||
.. index:: fix ave/histo
|
||||
.. index:: fix ave/histo/weight
|
||||
|
||||
fix ave/histo command
|
||||
=====================
|
||||
|
|
|
|||
|
|
@ -1,4 +1,5 @@
|
|||
.. index:: fix bond/create
|
||||
.. index:: fix bond/create/angle
|
||||
|
||||
fix bond/create command
|
||||
=======================
|
||||
|
|
|
|||
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in New Issue