make subheaders and typesetting more consistent

``liblammps.a`` and ``liblammps.so``\ , which point to the specific

``liblammps_machine.a/so`` files.

**CMake and make info**\ :

CMake and make info

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

Note that for creating a shared library, all the libraries it depends on

must be compiled to be compatible with shared libraries.  This should be

.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html

.. _sphinx: https://sphinx-doc.org

**Documentation make option**\ :

Documentation make option

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

The following make commands can be issued in the doc folder of the

LAMMPS source distribution.

   current LAMMPS version (HTML and PDF files), from the website

   `download page <https://lammps.sandia.gov/download.html>`_.

**CMake build option**\ :

CMake build option

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

It is also possible to create the HTML version of the manual within

the :doc:`CMake build directory <Build_cmake>`.  The reason for this

Some tools described in :doc:`Auxiliary tools <Tools>` can be built directly

using CMake or Make.

**CMake build3**\ :

CMake build

^^^^^^^^^^^

.. code-block:: bash

The generated binaries will also become part of the LAMMPS installation

(see below).

**Traditional make**\ :

Traditional make

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

.. code-block:: bash

that you may need super-user privileges (e.g. sudo) if the directory

you want to copy files to is protected.

**CMake build**\ :

CMake build

^^^^^^^^^^^

.. code-block:: bash

   make                        # perform make after CMake command

   make install                # perform the installation into prefix

**Traditional make**\ :

Traditional make

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

There is no "install" option in the ``src/Makefile`` for LAMMPS.  If

you wish to do this you will need to first build LAMMPS, then manually

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

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

**CMake variables**\ :

CMake build

^^^^^^^^^^^

.. code-block:: bash

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

   -D MKL_LIBRARIES=path

**Makefile.machine settings**\ :

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

could be changed.

.. code-block:: make

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 and make info**\ :

CMake build

^^^^^^^^^^^

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

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

version 3.X; the legacy version 2.1.X is no longer supported.

Building FFTW for your box should be as simple as ``./configure; make;

make install``\ .  The install command typically requires root privileges

make install``.  The install command typically requires root privileges

(e.g. invoke it via sudo), unless you specify a local directory with

the "--prefix" option of configure.  Type ``./configure --help`` to see

various options.

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

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

**CMake variable**\ :

CMake build

^^^^^^^^^^^

.. code-block:: bash

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

**Makefile.machine setting**\ :

Traditional build

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

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

machine Makefile.

.. code-block:: make

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

**CMake and make info**\ :

CMake and make info

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

The default "smallbig" setting allows for simulations with:

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

following settings:

**CMake variables**\ :

CMake build

^^^^^^^^^^^

.. code-block:: bash

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

   -D FFMPEG_EXECUTABLE=path   # path to ffmpeg executable

**Makefile.machine settings**\ :

Traditional make

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

.. code-block:: make

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**\ :

CMake and make info

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

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

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

gzip compression by several LAMMPS commands, including

:doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.

**CMake variables**\ :

CMake build

^^^^^^^^^^^

.. code-block:: bash

                            # default is yes if CMake can find gzip, else no

   -D GZIP_EXECUTABLE=path  # path to gzip executable if CMake cannot find it

**Makefile.machine setting**\ :

Traditional make

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

.. code-block:: make

   LMP_INC = -DLAMMPS_GZIP

**CMake and make info**\ :

CMake and make info

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

This option requires that your machine supports the "popen()" function

in the standard runtime library and that a gzip executable can be

instructions efficiently, however, requires memory blocks being

aligned on 64-byte boundaries.

**CMake variable**\ :

CMake build

^^^^^^^^^^^

.. code-block:: bash

compiling LAMMPS for Windows systems, malloc() will always be used

and this setting ignored.

**Makefile.machine setting**\ :

Traditional make

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

.. code-block:: make

to a "long" data type, which should be the desired 8-byte integer on

those systems:

**CMake variable**\ :

CMake build

^^^^^^^^^^^

.. code-block:: bash

   -D LAMMPS_LONGLONG_TO_LONG=value     # yes or no (default)

**Makefile.machine setting**\ :

Traditional make

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

.. code-block:: make

e.g. to Python. Of course, the calling code has to be set up to

*catch* exceptions thrown from within LAMMPS.

**CMake variable**\ :

CMake build

^^^^^^^^^^^

.. code-block:: bash

   -D LAMMPS_EXCEPTIONS=value        # yes or no (default)

**Makefile.machine setting**\ :

Traditional make

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

.. code-block:: make