big update

	@rm -rf html/JPG

	@cp -r src/PDF html/PDF

	@mkdir -p html/JPG

	@cp `grep -A2 '\.\. .*\(image\|figure\)::' src/*.rst | grep ':target:' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/

	@cp `grep -A2 '\.\. .*\(image\|figure\)::' src/*.rst | grep ':target: JPG' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/

	@rm -rf html/PDF/.[sg]*

	@mkdir -p html/_static/mathjax

	@cp -r $(MATHJAX)/es5 html/_static/mathjax/

		$(VIRTUALENV) -p $(PYTHON) $(VENV); \

		. $(VENV)/bin/activate; \

		pip install --upgrade pip; \

		pip install Sphinx; \

		pip install sphinxcontrib-spelling ;\

		pip install breathe; \

		pip install --use-feature=2020-resolver -r requirements.txt; \

		deactivate;\

	)

.TH LAMMPS "15 April 2020" "2020-04-15"

.TH LAMMPS "21 August 2020" "2020-08-21"

.SH NAME

.B LAMMPS

\- Molecular Dynamics Simulator.

Sphinx

sphinxcontrib-spelling

breathe

Pygments

included in the build.

You can tell CMake to look for a specific compiler with setting CMake

variable during configuration.  For a few common choices, there are also

presets in the ``cmake/presets`` folder.  For convenience, there is a

``CMAKE_TUNE_FLAGS`` variable that can be set to apply global compiler

options.  More on that below, but you can also specify the corresponding

``CMAKE_*_FLAGS`` variables individually if you want to experiment with

alternate optimization flags.  You should specify all 3 compilers, so

that the (few) LAMMPS source files written in C or Fortran are built

with a compiler consistent with the one used for the C++ files:

variables (listed below) during configuration.  For a few common

choices, there are also presets in the ``cmake/presets`` folder.  For

convenience, there is a ``CMAKE_TUNE_FLAGS`` variable that can be set to

apply global compiler options (applied to compilation only), to be used

for adding compiler or host specific optimization flags in addition to

the "flags" variables listed below. You may also specify the

corresponding ``CMAKE_*_FLAGS`` variables individually, if you want to

experiment with alternate optimization flags.  You should specify all 3

compilers, so that the (few) LAMMPS source files written in C or Fortran

are built with a compiler consistent with the one used for the C++

files:

.. code-block:: bash

In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add

compiler flags to tune for optimal performance on given hosts. By

default these are initialized to some compiler specific flags, to

optimize the LAMMPS executable with optimizations and instructions

available on the host where LAMMPS is compiled. For example, for Intel

compilers this would be ``-xHost`` and for GNU compilers this would be

``-march=native``. To turn these flags off, do ``-D CMAKE_TUNE_FLAGS=``.

default this variable is empty.

.. note::

``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

``cmake .`` and then compile again. The included dependency tracking

should make certain that only the necessary subset of files are

re-compiled.  You can also delete compiled objects, libraries and

executables with ``cmake --build . clean`` (or ``make clean``).

executables with ``cmake --build . --target clean`` (or ``make clean``).

After compilation, you may optionally install the LAMMPS executable into

your system with: