Merge pull request #2043 from ellio167/ubuntu-install-docs

   * :doc:`msd/chunk <compute_msd_chunk>`

   * :doc:`msd/chunk <compute_msd_chunk>`

   * :doc:`msd/nongauss <compute_msd_nongauss>`

   * :doc:`msd/nongauss <compute_msd_nongauss>`

   * :doc:`omega/chunk <compute_omega_chunk>`

   * :doc:`omega/chunk <compute_omega_chunk>`

   * :doc:`orientorder/atom <compute_orientorder_atom>`

   * :doc:`orientorder/atom (k) <compute_orientorder_atom>`

   * :doc:`pair <compute_pair>`

   * :doc:`pair <compute_pair>`

   * :doc:`pair/local <compute_pair_local>`

   * :doc:`pair/local <compute_pair_local>`

   * :doc:`pe <compute_pe>`

   * :doc:`pe <compute_pe>`

.. code-block:: bash

.. code-block:: bash

   cmake -C ../cmake/preset/minimal.cmake -D PKG_MISC=on ../cmake

   cmake -C ../cmake/presets/minimal.cmake -D PKG_MISC=on ../cmake

   cmake -C ../cmake/preset/clang.cmake -C ../cmake/preset/most.cmake ../cmake

   cmake -C ../cmake/presets/clang.cmake -C ../cmake/presets/most.cmake ../cmake

   cmake -C ../cmake/preset/minimal.cmake -D BUILD_MPI=off ../cmake

   cmake -C ../cmake/presets/minimal.cmake -D BUILD_MPI=off ../cmake

The first command will install the packages ``KSPACE``, ``MANYBODY``,

The first command will install the packages ``KSPACE``, ``MANYBODY``,

``MOLECULE``, ``RIGID`` and ``MISC``; the first four from the preset

``MOLECULE``, ``RIGID`` and ``MISC``; the first four from the preset

.. code-block:: bash

.. code-block:: bash

   cmake -C ../cmake/preset/minimal.cmake ../cmake

   cmake -C ../cmake/presets/minimal.cmake ../cmake

   cmake -D PKG_MISC=on .

   cmake -D PKG_MISC=on .

will achieve the same configuration like in the first example above.  In

will achieve the same configuration like in the first example above.  In

up-to-date with the current version of LAMMPS by simply updating your

up-to-date with the current version of LAMMPS by simply updating your

operating system.

operating system.

To install the appropriate personal-package archive (PPA), do the

To install the appropriate personal-package archives (PPAs), do the

following once:

following once:

.. code-block:: bash

.. code-block:: bash

   $ sudo add-apt-repository ppa:gladky-anton/lammps

   $ sudo add-apt-repository ppa:gladky-anton/lammps

   $ sudo add-apt-repository ppa:openkim/latest

   $ sudo apt-get update

   $ sudo apt-get update

To install LAMMPS do the following once:

To install LAMMPS do the following once:

   $ sudo apt-get install lammps-daily

   $ sudo apt-get install lammps-daily

This downloads an executable named "lmp_daily" to your box, which

This downloads an executable named ``lmp_daily`` to your box, which

can then be used in the usual way to run input scripts:

can then be used in the usual way to run input scripts:

.. code-block:: bash

.. code-block:: bash

   $ sudo apt-get install lammps-daily-doc

   $ sudo apt-get install lammps-daily-doc

which will download the doc files in

which will download the doc files in

/usr/share/doc/lammps-daily-doc/doc and example problems in

``/usr/share/doc/lammps-daily-doc/doc`` and example problems in

/usr/share/doc/lammps-doc/examples.

``/usr/share/doc/lammps-doc/examples``.

Note that you may still wish to download the tarball to get potential

To get a copy of the current potentials files:

files and auxiliary tools.

To un-install LAMMPS, do the following:

.. code-block:: bash

   $ sudo apt-get install lammps-daily-data

which will download the potentials files to

``/usr/share/lammps-daily/potentials``.  The ``lmp_daily`` binary is

hard-coded to look for potential files in this directory (it does not

use the `LAMMPS_POTENTIALS` environment variable, as described

in :doc:`pair_coeff <pair_coeff>` command).

The ``lmp_daily`` binary is built with the :ref:`KIM package <kim>` which

results in the above command also installing the `kim-api` binaries when LAMMPS

is installed.  In order to use potentials from `openkim.org <openkim_>`_, you

can install the `openkim-models` package

.. code-block:: bash

.. code-block:: bash

   $ sudo apt-get remove lammps-daily

   $ sudo apt-get install openkim-models

Note that the lammps-daily executable is built with the following

To un-install LAMMPS, do the following:

sequence of make commands, as if you had done the same with the

unpacked tarball files in the src directory:

.. code-block:: bash

.. code-block:: bash

    $ make yes-all

   $ sudo apt-get remove lammps-daily

    $ make no-lib

    $ make mpi

Thus it builds with FFTW3 and OpenMPI.

Please use ``lmp_daily -help`` to see which compilation options, packages,

and styles are included in the binary.

Thanks to Anton Gladky (gladky.anton at gmail.com) for setting up this

Thanks to Anton Gladky (gladky.anton at gmail.com) for setting up this

Ubuntu package capability.

Ubuntu package capability.

lammps-openmpi-devel), the header for compiling programs using

lammps-openmpi-devel), the header for compiling programs using

the C library interface (lammps-headers), and the LAMMPS python

the C library interface (lammps-headers), and the LAMMPS python

module for Python 3. All packages can be installed at the same

module for Python 3. All packages can be installed at the same

time and the name of the LAMMPS executable is *lmp* and *lmp_openmpi*

time and the name of the LAMMPS executable is ``lmp`` and ``lmp_openmpi``

or *lmp_mpich* respectively.  By default, *lmp* will refer to the

or ``lmp_mpich`` respectively.  By default, ``lmp`` will refer to the

serial executable, unless one of the MPI environment modules is loaded

serial executable, unless one of the MPI environment modules is loaded

("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64").

(``module load mpi/mpich-x86_64`` or ``module load mpi/openmpi-x86_64``).

Then the corresponding parallel LAMMPS executable can be used.

Then the corresponding parallel LAMMPS executable can be used.

The same mechanism applies when loading the LAMMPS python module.

The same mechanism applies when loading the LAMMPS python module.

To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do:

To install LAMMPS with OpenMPI and run an input ``in.lj`` with 2 CPUs do:

.. code-block:: bash

.. code-block:: bash

   $ module load mpi/openmpi-x86_64

   $ module load mpi/openmpi-x86_64

   $ mpirun -np 2 lmp -in in.lj

   $ mpirun -np 2 lmp -in in.lj

The "dnf install" command is needed only once. In case of a new LAMMPS

The ``dnf install`` command is needed only once. In case of a new LAMMPS

stable release, "dnf update" will automatically update to the newer

stable release, ``dnf update`` will automatically update to the newer

version as soon at the RPM files are built and uploaded to the download

version as soon at the RPM files are built and uploaded to the download

mirrors. The "module load" command is needed once per (shell) session

mirrors. The ``module load`` command is needed once per (shell) session

or shell terminal instance, unless it is automatically loaded from the

or shell terminal instance, unless it is automatically loaded from the

shell profile.

shell profile.

   $ dnf install openkim-models

   $ dnf install openkim-models

Please use "lmp -help" to see which compilation options, packages,

Please use ``lmp -help`` to see which compilation options, packages,

and styles are included in the binary.

and styles are included in the binary.

Thanks to Christoph Junghans (LANL) for making LAMMPS available in Fedora.

Thanks to Christoph Junghans (LANL) for making LAMMPS available in Fedora.

for use with Red Hat Enterprise Linux (RHEL) or CentOS version 7.x

for use with Red Hat Enterprise Linux (RHEL) or CentOS version 7.x

and compatible Linux distributions. Names of packages, executable,

and compatible Linux distributions. Names of packages, executable,

and content are the same as described above for Fedora Linux.

and content are the same as described above for Fedora Linux.

But RHEL/CentOS 7.x uses the "yum" package manager instead of "dnf"

But RHEL/CentOS 7.x uses the ``yum`` package manager instead of ``dnf``

in Fedora 28.

in Fedora 28.

Please use "lmp -help" to see which compilation options, packages,

Please use ``lmp -help`` to see which compilation options, packages,

and styles are included in the binary.

and styles are included in the binary.

Thanks to Christoph Junghans (LANL) for making LAMMPS available in EPEL.

Thanks to Christoph Junghans (LANL) for making LAMMPS available in EPEL.

   $ zypper install lammps

   $ zypper install lammps

This includes support for OpenMPI. The name of the LAMMPS executable

This includes support for OpenMPI. The name of the LAMMPS executable

is *lmp*\ . Thus to run an input in parallel on 2 CPUs you would do:

is ``lmp``. Thus to run an input in parallel on 2 CPUs you would do:

.. code-block:: bash

.. code-block:: bash

   $ mpirun -np 2 lmp -in in.lj

   $ mpirun -np 2 lmp -in in.lj

Please use "lmp -help" to see which compilation options, packages,

Please use ``lmp -help`` to see which compilation options, packages,

and styles are included in the binary.

and styles are included in the binary.

The LAMMPS binary is built with the :ref:`KIM package <kim>` which

The LAMMPS binary is built with the :ref:`KIM package <kim>` which

================================

================================

compute orientorder/atom/kk command

compute orientorder/atom/kk command

=======================

===================================

Syntax

Syntax

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