load sphinx extension for content in tabs with html and for transforming them...

library is included with LAMMPS but other libraries can be faster.

LAMMPS can use them if they are available on your system.

CMake build

^^^^^^^^^^^

.. tabs::

   .. tab:: CMake build

      .. code-block:: bash

         an exception to the rule that all CMake variables can be specified

         with lower-case values.

Usually these settings are all that is needed.  If FFTW3 is selected,

then CMake will try to detect, if threaded FFTW libraries are available

and enable them by default.  This setting is independent of whether

OpenMP threads are enabled and a packages like KOKKOS or USER-OMP is

used.  If CMake cannot detect the FFT library, you can set these variables

to assist:

      Usually these settings are all that is needed.  If FFTW3 is

      selected, then CMake will try to detect, if threaded FFTW

      libraries are available and enable them by default.  This setting

      is independent of whether OpenMP threads are enabled and a

      packages like KOKKOS or USER-OMP is used.  If CMake cannot detect

      the FFT library, you can set these variables to assist:

      .. code-block:: bash

         -D FFT_MKL_THREADS=on       # enable using threaded FFTs with MKL libraries

         -D MKL_LIBRARIES=path

Traditional make

^^^^^^^^^^^^^^^^

   .. tab:: Traditional make

      To change the FFT library to be used and its options, you have to edit

      your machine Makefile. Below are examples how the makefile variables

         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_PACK_ARRAY    # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY

                                       # default is FFT_PACK_ARRAY if not specified

      .. code-block:: make

         FFT_LIB =       -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core      # MKL with GNU compiler, threaded interface

         FFT_LIB =       -lmkl_rt            # MKL with automatic runtime selection of interface libs

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 files in its default search path.

You must specify ``FFT_LIB`` with the appropriate FFT libraries to include in the link.

CMake build

^^^^^^^^^^^

      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

      files in its default search path.  You must specify ``FFT_LIB``

      with the appropriate FFT libraries to include in the link.

The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS

distribution.  It is portable across all platforms.  Depending on the size

.. _size:

Size of LAMMPS integer types

------------------------------------

Size of LAMMPS integer types and size limits

--------------------------------------------

LAMMPS has a few integer data types which can be defined as either

4-byte (= 32-bit) or 8-byte (= 64-bit) integers at compile time.

The default setting of "smallbig" is almost always adequate.

CMake build

^^^^^^^^^^^

.. tabs::

   .. tab:: CMake build

      .. code-block:: bash

         -D LAMMPS_SIZES=value   # smallbig (default) or bigbig or smallsmall

Traditional build

^^^^^^^^^^^^^^^^^

   .. tab:: Traditional build

      If you want a setting different from the default, you need to edit your

      machine Makefile.

The default setting is ``-DLAMMPS_SMALLBIG`` if nothing is specified

CMake and make info

^^^^^^^^^^^^^^^^^^^

LAMMPS system size restrictions

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

The default "smallbig" setting allows for simulations with:

angles, dihedrals, etc).  Thus if you model a molecular system with

more than 2 billion atoms, you need the "bigbig" setting.

Image flags store 3 values per atom which count the number of times an

atom has moved through the periodic box in each dimension.  See the

:doc:`dump <dump>` doc page for a discussion.  If an atom moves through

the periodic box more than this limit, the value will "roll over",

e.g. from 511 to -512, which can cause diagnostics like the

mean-squared displacement, as calculated by the :doc:`compute msd <compute_msd>` command, to be faulty.

Note that the USER-ATC package and the USER-INTEL package are currently

not compatible with the "bigbig" setting. Also, there are limitations

when using the library interface. Some functions with known issues

have been replaced by dummy calls printing a corresponding error rather

than crashing randomly or corrupting data.

Regardless of the total system size limits, the maximum number of atoms

per MPI rank (local + ghost atoms) is limited to 2 billion for atomic

systems and 500 million for systems with bonds (due to using the 2

upper bits of the local atom index for storing special bonds labels).

Image flags store 3 values per atom in a single integer which count the

number of times an atom has moved through the periodic box in each

dimension.  See the :doc:`dump <dump>` doc page for a discussion.  If an

atom moves through the periodic box more than this limit, the value will

"roll over", e.g. from 511 to -512, which can cause diagnostics like the

mean-squared displacement, as calculated by the :doc:`compute msd

<compute_msd>` command, to be faulty.

Note that the USER-ATC package is currently not compatible with the

"bigbig" setting. Also, there are limitations when using the library

interface. Some functions with known issues have been replaced by dummy

calls printing a corresponding error rather than crashing randomly or

corrupting data.

Also note that the GPU package requires its lib/gpu library to be

compiled with the same size setting, or the link will fail.  A CMake

outputs movie files in MPEG format.  Using these options requires the

following settings:

CMake build

^^^^^^^^^^^

.. tabs::

   .. tab:: CMake build

      .. code-block:: bash

         -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 find

the graphics header, library, executable files, you can set these

variables:

      Usually these settings are all that is needed.  If CMake cannot

      find the graphics header, library, executable files, you can set

      these variables:

      .. code-block:: bash

         -D ZLIB_LIBRARIES=path      # path to libz.a (.so) file

         -D FFMPEG_EXECUTABLE=path   # path to ffmpeg executable

Traditional make

^^^^^^^^^^^^^^^^

   .. tab:: Traditional make

      .. code-block:: make

      As with CMake, you do not need to set ``JPG_INC`` or ``JPG_PATH``,

      if make can find the graphics header and library files.  You must

specify ``JPG_LIB``

with a list of graphics libraries to include in the link.  You must

insure ffmpeg is in a directory where LAMMPS can find it at runtime,

that is a directory in your PATH environment variable.

CMake and make info

^^^^^^^^^^^^^^^^^^^

      specify ``JPG_LIB`` with a list of graphics libraries to include

      in the link.  You must insure ffmpeg is in a directory where

      LAMMPS can find it at runtime, that is a directory in your PATH

      environment variable.

Using ``ffmpeg`` to output movie files requires that your machine

supports the "popen" function in the standard runtime library.

def replace_tabs_handler(app, docname, source):

    """ When builder is not 'html', remove 'tabs' directive

    and replace 'tab' directive with 'admonition'"""

    if app.builder.name != 'html':

        for i in range(len(source)):

            str = source[i].replace('.. tabs::','')

            str = str.replace('.. tab::','.. admonition::')

            source[i] = str

def setup(app):

    app.connect('source-read', replace_tabs_handler)

    return {

        'version': '0.1',

        'parallel_read_safe': True,

        'parallel_write_safe': True,

    }

Sphinx

sphinxcontrib-spelling

git+https://github.com/akohlmey/sphinx-fortran@parallel-read

sphinx_tabs

breathe

Pygments

    'sphinx.ext.imgmath',

    'sphinx.ext.autodoc',

    'sphinxfortran.fortran_domain',

    'sphinx_tabs.tabs',

    'table_from_list',

    'tab_or_note',

    'breathe',

]

# 2017-12-07: commented out, since this package is broken with Sphinx 16.x