replace more parsed-literal with code-block sections

environment (named `my-lammps-env` or whatever you prefer) for your lammps

install:

.. parsed-literal::

.. code-block:: bash

   % conda config --add channels conda-forge

   % conda create -n my-lammps-env

Then, you can install lammps on your system with the following command:

.. parsed-literal::

.. code-block:: bash

   % conda activate my-lammps-env

   % conda install lammps

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

install the `openkim-models` package

.. parsed-literal::

.. code-block:: bash

   % conda install openkim-models

up the Conda capability.

.. _conda_forge_lammps: https://github.com/conda-forge/lammps-feedstock/issues

.. _openkim: https://openkim.org

.. _conda: https://docs.conda.io/en/latest/index.html

.. _mini_conda_install: https://docs.conda.io/en/latest/miniconda.html

Download the LAMMPS source with Git

Download the LAMMPS source with git

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

All LAMMPS development is coordinated through the "LAMMPS GitHub

* You can submit your new features back to GitHub for inclusion in

  LAMMPS.

You must have `Git <git_>`_ installed on your system to communicate with

the public Git server for LAMMPS.

You must have `git <git_>`_ installed on your system to communicate with

the public git server for LAMMPS.

.. warning::

   As of October 2016, the official home of public LAMMPS development is

   on GitHub.  The previously advertised LAMMPS git repositories on

   git.lammps.org and bitbucket.org are now deprecated, may not be

   up-to-date, and may go away at any time.

   git.lammps.org and bitbucket.org are now deprecated, and may go away at any time.

.. _git: https://git-scm.com

You can follow LAMMPS development on 3 different Git branches:

You can follow LAMMPS development on 3 different git branches:

* **stable**   :  this branch is updated with every stable release

* **unstable** :  this branch is updated with every patch release

* **master**   :  this branch continuously follows ongoing development

To access the Git repositories on your box, use the clone command to

To access the git repositories on your box, use the clone command to

create a local copy of the LAMMPS repository with a command like:

.. parsed-literal::

.. code-block:: bash

   git clone -b unstable https://github.com/lammps/lammps.git mylammps

   $ git clone -b unstable https://github.com/lammps/lammps.git mylammps

where "mylammps" is the name of the directory you wish to create on

your machine and "unstable" is one of the 3 branches listed above.

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

up-to-date by typing the following git commands from within the

"mylammps" directory:

.. parsed-literal::

.. 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 pull

   $ 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 pull

Doing a "pull" will not change any files you have added to the LAMMPS

directory structure.  It will also not change any existing LAMMPS

files you have edited, unless those files have changed in the

repository.  In that case, Git will attempt to merge the new

repository.  In that case, git will attempt to merge the new

repository file with your version of the file and tell you if there

are any conflicts.  See the Git documentation for details.

are any conflicts.  See the git documentation for details.

If you want to access a particular previous release version of LAMMPS,

you can instead "checkout" any version with a published tag. See the

output of "git tag -l" for the list of tags.  The Git command to do

output of "git tag -l" for the list of tags.  The git command to do

this is as follows.

.. code-block:: bash

.. parsed-literal::

   git checkout tagID

   $ git checkout tagID

Stable versions and what tagID to use for a particular stable version

are discussed on :doc:`this page <Errors_bugs>`.  Note that this command

changed.  To do this, you should cd to the src directory and type:

.. parsed-literal::

.. code-block:: bash

   make purge             # remove any deprecated src files

   make package-update    # sync package files with src files

   make foo               # re-build for your machine (mpi, serial, etc)

   $ make purge             # remove any deprecated src files

   $ 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,

after a patch has been installed.

| :ref:`Arch Linux build-script <arch>`

|

----------

.. _ubuntu:

Pre-built Ubuntu Linux executables

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

following once:

.. code-block:: bash

.. parsed-literal::

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

   sudo apt-get update

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

   $ sudo apt-get update

To install LAMMPS do the following once:

.. code-block:: bash

.. parsed-literal::

   sudo apt-get install lammps-daily

   $ sudo apt-get install lammps-daily

This downloads an executable named "lmp\_daily" to your box, which

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

.. code-block:: bash

.. parsed-literal::

   lmp_daily -in in.lj

   $ lmp_daily -in in.lj

To update LAMMPS to the most current version, do the following:

.. code-block:: bash

.. parsed-literal::

   sudo apt-get update

   $ sudo apt-get update

which will also update other packages on your system.

To get a copy of the current documentation and examples:

.. code-block:: bash

.. parsed-literal::

   sudo apt-get install lammps-daily-doc

   $ sudo apt-get install lammps-daily-doc

which will download the doc files in

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

To un-install LAMMPS, do the following:

.. code-block:: bash

.. parsed-literal::

   sudo apt-get remove lammps-daily

   $ sudo apt-get remove lammps-daily

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

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

unpacked tarball files in the src directory:

make yes-all; make no-lib; make openmpi

.. code-block:: bash

    $ make yes-all

    $ make no-lib

    $ make mpi

Thus it builds with FFTW3 and OpenMPI.

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

Ubuntu package capability.

----------

.. _fedora:

Pre-built Fedora Linux executables

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

.. code-block:: bash

.. parsed-literal::

   dnf install lammps-openmpi

   module load mpi/openmpi-x86_64

   mpirun -np 2 lmp -in in.lj

   $ dnf install lammps-openmpi

   $ module load mpi/openmpi-x86_64

   $ mpirun -np 2 lmp -in in.lj

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

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

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

can install the `openkim-models` package

.. parsed-literal::

.. code-block:: bash

   dnf install openkim-models

   $ dnf install openkim-models

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

and styles are included in the binary.

----------

.. _epel:

Pre-built EPEL Linux executable

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

----------

.. _opensuse:

Pre-built OpenSuse Linux executable

A pre-built LAMMPS package for stable releases is available

in OpenSuse as of Leap 15.0. You can install the package with:

.. code-block:: bash

.. parsed-literal::

   zypper install lammps

   $ zypper install lammps

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:

.. code-block:: bash

.. parsed-literal::

   mpirun -np 2 lmp -in in.lj

   $ mpirun -np 2 lmp -in in.lj

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

and styles are included in the binary.

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

can install the `openkim-models` package

.. parsed-literal::

.. code-block:: bash

   zypper install openkim-models

   $ zypper install openkim-models

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

----------

.. _gentoo:

Gentoo Linux executable

typing:

.. parsed-literal::

.. code-block:: bash

   % emerge --ask lammps

Certain LAMMPS packages can be enable via USE flags, type

.. parsed-literal::

.. code-block:: bash

   % equery uses lammps

Thanks to Nicolas Bock and Christoph Junghans (LANL) for setting up

this Gentoo capability.

----------

.. _arch:

Archlinux build-script

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

LAMMPS is available via Arch's unofficial Arch User repository (AUR).

There are three scripts available, named lammps, lammps-beta and lammps-git.

They respectively package the stable, patch and git releases.

To install, you will need to have the git package installed. You may use

any of the above names in-place of lammps.

.. parsed-literal::

.. code-block:: bash

   $ git clone https://aur.archlinux.org/lammps.git

   $ cd lammps

   $ makepkg -s

   # makepkg -i

   $ makepkg -i

To update, you may repeat the above, or change into the cloned directory,

and execute the following, after which, if there are any changes, you may

use makepkg as above.

.. parsed-literal::

.. code-block:: bash

   $ git pull

the following commands:

.. parsed-literal::

.. code-block:: bash

   % brew install lammps

Lennard-Jones benchmark file:

.. parsed-literal::

.. code-block:: bash

   % brew test lammps -v

install the `openkim-models` package

.. parsed-literal::

.. code-block:: bash

   % brew install openkim-models

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

It is easy to stay current with the most recent LAMMPS patch releases

if you use Git or SVN to track LAMMPS development.  Instructions for

if you use git or SVN to track LAMMPS development.  Instructions for

how to stay current are on the :doc:`Install git <Install_git>` and

:doc:`Install svn <Install_svn>` doc pages.

.. note::

   You should not apply patch files to a local Git or SVN repo of

   LAMMPS, only to an unpacked tarball.  Use Git and SVN commands to

   You should not apply patch files to a local git or SVN repo of

   LAMMPS, only to an unpacked tarball.  Use git and SVN commands to

   update repo versions of LAMMPS.

Here are the steps to apply a patch file.  Note that if your version

  LAMMPS directory, where the redirected file is the name of the patch

  file.

  .. parsed-literal::

  .. code-block:: bash

     patch -bp1 < patch.12Dec16

     $ patch -bp1 < patch.12Dec16

* A list of updated files print out to the screen.  The -b switch

  creates backup files of your originals (e.g. src/force.cpp.orig), so

  command removes deprecated src files if any were removed by the patch

  from package sub-directories.

  .. parsed-literal::

  .. code-block:: bash

     make purge

     make package-update

     $ make purge

     $ make package-update

* Re-build LAMMPS via the "make" command.