Merge branch 'master' into progguide

from within Windows and from there on, you can pretty much use that

shell like you are running on an Ubuntu Linux machine (e.g. installing

software via apt-get and more). For more details on that, please

see :doc:`this tutorial <Howto_bash>`

see :doc:`this tutorial <Howto_wsl>`

.. _gnu:

   Howto_cmake

   Howto_github

   Howto_pylammps

   Howto_bash

   Howto_wsl

General howto

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

Using LAMMPS with Bash on Windows

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

**written by Richard Berger**

----------

Starting with Windows 10 you can install Linux tools directly in Windows. This

allows you to compile LAMMPS following the same procedure as on a real Ubuntu

Linux installation. Software can be easily installed using the package manager

via apt-get and all files are accessible in both the Windows Explorer and your

Linux shell (bash). This avoids switching to a different operating system or

installing a virtual machine. Everything runs on Windows.

.. seealso::

   You can find more detailed information at the `Windows Subsystem for Linux Installation Guide for Windows 10 <https://docs.microsoft.com/en-us/windows/wsl/install-win10>`_.

Installing Bash on Windows

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

Prerequisites

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

* Windows 10 (64bit only)

* Latest updates installed

Enable developer mode

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

You enable this feature by first opening Windows Settings and enabling

Developer mode. Go to the Windows settings and search for "developer". This

will allow you to install software which comes from outside of the Windows

Store.  You might be prompted to reboot your compute. Please do so.

.. image:: JPG/bow_tutorial_01_small.png

   :target: JPG/bow_tutorial_01.png

.. image:: JPG/bow_tutorial_02_small.png

   :target: JPG/bow_tutorial_02.png

.. image:: JPG/bow_tutorial_03_small.png

   :target: JPG/bow_tutorial_03.png

Install Windows Subsystem for Linux

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

Next you must ensure that the Window Subsystem for Linux is installed. Again,

search for "enable windows features" in the Settings dialog. This opens a

dialog with a list of features you can install. Add a checkmark to Windows

Subsystem for Linux (Beta) and press OK.

.. image:: JPG/bow_tutorial_04_small.png

   :target: JPG/bow_tutorial_04.png

.. image:: JPG/bow_tutorial_05.png

   :target: JPG/bow_tutorial_05.png

Install Bash for Windows

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

After installation completes, type "bash" in the Windows Start menu search.

Select the first found option. This will launch a command-line window which

will prompt you about installing Ubuntu on Windows. Confirm with "y" and press

enter. This will then download Ubuntu for Windows.

.. image:: JPG/bow_tutorial_06.png

.. image:: JPG/bow_tutorial_07.png

During installation, you will be asked for a new password. This will be used

for installing new software and running commands with sudo.

.. image:: JPG/bow_tutorial_08.png

Type exit to close the command-line window.

Go to the Start menu and type "bash" again. This time you will see a "Bash on

Ubuntu on Windows" Icon. Start this program.

.. image:: JPG/bow_tutorial_09.png

Congratulations, you have installed **Bash on Ubuntu on Windows**\ .

.. image:: JPG/bow_tutorial_10.png

----------

Compiling LAMMPS in Bash on Windows

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

The installation of LAMMPS in this environment is identical to working inside

of a real Ubuntu Linux installation. At the time writing, it uses Ubuntu 16.04.

Installing prerequisite packages

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

First upgrade all existing packages using

.. code-block:: bash

   sudo apt update

   sudo apt upgrade -y

Next install the following packages, which include compilers and libraries

needed for various LAMMPS features:

.. code-block:: bash

   sudo apt install -y build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng-dev python-dev python-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tools

Files in Ubuntu on Windows

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

When you launch "Bash on Ubuntu on Windows" you will start out in your Linux

user home directory /home/[username]\ . You can access your Windows user directory

using the /mnt/c/Users/[username] folder.

Download LAMMPS

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

Obtain a copy of the LAMMPS code and go into it using "cd"

Option 1: Downloading LAMMPS tarball using wget

"""""""""""""""""""""""""""""""""""""""""""""""

.. code-block:: bash

   wget https://lammps.sandia.gov/tars/lammps-stable.tar.gz

   tar xvzf lammps-stable.tar.gz

   cd lammps-31Mar17

Option 2: Obtaining LAMMPS code from GitHub

"""""""""""""""""""""""""""""""""""""""""""

.. code-block:: bash

   git clone https://github.com/lammps/lammps.git

   cd lammps

Compiling LAMMPS

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

At this point you can compile LAMMPS like on Ubuntu Linux.

Compiling serial version

""""""""""""""""""""""""

.. code-block:: bash

   cd src/

   make -j 4 serial

This will create an executable called lmp_serial in the src/ directory

Compiling MPI version

"""""""""""""""""""""

.. code-block:: bash

   cd src/

   make -j 4 mpi

This will create an executable called lmp_mpi in the src/ directory

----------

Finally, please note the absolute path of your src folder. You can get this using

.. code-block:: bash

   pwd

or

.. code-block:: bash

   echo $PWD

To run any examples you need the location of the executable. For now, let us

save this location in a temporary variable

.. code-block:: bash

   LAMMPS_DIR=$PWD

----------

Running an example script

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

Once compiled you can execute some of the LAMMPS examples. Switch into the

examples/melt folder

.. code-block:: bash

   cd ../examples/melt

The full path of the serial executable is $LAMMPS_DIR/lmp_serial, while the mpi

version is $LAMMPS_DIR/lmp_mpi. You can run the melt example with either

version as follows:

.. code-block:: bash

   $LAMMPS_DIR/lmp_serial -in in.melt

or

.. code-block:: bash

   mpirun -np 4 $LAMMPS_DIR/lmp_mpi -in in.melt

Note the use of our variable $LAMMPS_DIR, which expands into the full path of

the LAMMPS src folder we saved earlier.

Adding your executable directory to your PATH

"""""""""""""""""""""""""""""""""""""""""""""

You can avoid having to type the full path of your LAMMPS binary by adding its

parent folder to the PATH environment variable as follows:

.. code-block:: bash

   export PATH=$LAMMPS_DIR:$PATH

Input scripts can then be run like this:

.. code-block:: bash

   lmp_serial -in in.melt

or

.. code-block:: bash

   mpirun -np 4 lmp_mpi -in in.melt

However, this PATH variable will not persist if you close your bash window.

To persist this setting edit the $HOME/.bashrc file using your favorite editor

and add this line

.. code-block:: bash

   export PATH=/full/path/to/your/lammps/src:$PATH

**Example:**

For an executable lmp_serial with a full path

.. code-block:: bash

   /home/richard/lammps/src/lmp_serial

the PATH variable should be

.. code-block:: bash

   export PATH=/home/richard/lammps/src:$PATH

.. note::

   This should give you a jump start when trying to run LAMMPS on Windows.

   To become effective in this environment I encourage you to look into Linux

   tutorials explaining Bash and Basic Unix commands (e.g., `Linux Journey <https://linuxjourney.com>`_)

- Linux: any Terminal window will work

- MacOS X: launch the Terminal application.

- Windows 10: install and run the :doc:`Windows subsystem for Linux <Howto_bash>`

- Windows 10: install and run the :doc:`Windows Subsystem for Linux <Howto_wsl>`

We also assume that you have downloaded and unpacked a recent LAMMPS source code package

or used Git to create a clone of the LAMMPS sources on your compilation machine.

Using LAMMPS on Windows 10 with WSL

###################################

**written by Richard Berger**

----------

It's always been tricky for us to have LAMMPS users and developers work on

Windows. We primarily develop LAMMPS to run on Linux clusters. To teach

LAMMPS in workshop settings, we had to redirect Windows users to

Linux Virtual Machines such as VirtualBox or Unix-like compilation with

Cygwin.

With the latest updates in Windows 10 (Version 2004, Build 19041 or higher),

Microsoft has added a new way to work on Linux-based code. The Windows

Subsystem for Linux (WSL). With WSL Version 2, you now get a Linux Virtual

Machine that transparently integrates into Windows. All you need is to ensure

you have the latest Windows updates installed and enable this new feature.

Linux VMs are then easily installed using the Microsoft Store.

In this tutorial, I'll show you how to set up and compile LAMMPS for both serial

and MPI usage in WSL2.

Installation

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

Upgrade to the latest Windows 10

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

Type "Updates" in Windows Start and select "Check for Updates".

.. image:: img/wsl_tutorial/updates.png

   :scale: 50%

Install all pending updates and reboot your system as many times as

necessary. Continue until your Windows installation is updated.

.. image:: img/wsl_tutorial/windows_update.png

   :scale: 50%

Verify your system has at least **version 2004 and build 19041 or later**. You

can find this information by clicking on "OS build info".

.. image:: img/wsl_tutorial/osinfo.png

   :scale: 50%

Enable WSL

----------

Next, we must install two additional Windows features to enable WSL support.

Open a PowerShell window as an administrator. Type "PowerShell" in Windows

Start and select "Run as Administrator".

.. image:: img/wsl_tutorial/powershell.png

   :scale: 50%

Windows will ask you for administrator access. After you accept a new command

line window will appear. Type in the following command to install WSL:

.. code-block::

   dism.exe /online /enable-feature /featurename:Microsoft-Windows-Subsystem-Linux /all /norestart

.. image:: img/wsl_tutorial/wsl_install1.png

Next, enable the VirtualMachinePlatform feature using the following command:

.. code-block::

   dism.exe /online /enable-feature /featurename:VirtualMachinePlatform /all /norestart

.. image:: img/wsl_tutorial/wsl_install2.png

Finally, reboot your system.

Update WSL kernel component

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

Download and install the :download:`WSL Kernel Component Update <https://wslstorestorage.blob.core.windows.net/wslblob/wsl_update_x64.msi>`.

Afterwards, reboot your system.

Set WSL2 as default

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

Again, open PowerShell as administrator and run the following command:

.. code-block:: powershell

   wsl --set-default-version 2

This command ensures that all future Linux installations will use WSL version 2.

.. image:: img/wsl_tutorial/wsl_install3.png

Install a Linux Distribution

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

Next, we need to install a Linux distribution via the Microsoft Store.

Install `Ubuntu 20.04 LTS <ms-windows-store://pdp/?ProductId=9n6svws3rx71>`_.

Once installed, you can launch it like any other application from the Start

Menu.

.. image:: img/wsl_tutorial/ubuntu_in_store.png

   :scale: 50%

Initial Setup

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

The first time you launch the Ubuntu Linux console, it will prompt you for a

UNIX username and password. You will need this password to perform :code:`sudo`

commands later. Once completed, your Linux shell is ready for use. All your

actions and commands will run as the Linux user you specified.

.. image:: img/wsl_tutorial/first_login.png

   :scale: 50%

Windows Explorer / WSL integration

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

Your Linux installation will have its own Linux filesystem, which contains

the Ubuntu files. Your Linux user will have a regular Linux home directory in

:code:`/home/<USERNAME>`. This directory is different from your Windows User

directory. Windows and Linux filesystems are connected through WSL.

All hard drives in Windows are accessible in the :code:`/mnt` directory in Linux.

E.g., WSL maps the :code:`C` hard drive to the :code:`/mnt/c` directory. That means you

can access your Windows User directory in :code:`/mnt/c/Users/<WINDOWS_USERNAME>`.

The Windows Explorer can also access the Linux filesystem. To illustrate this

integration, open an Ubuntu console and navigate to a directory of your

choice. To view this location in Windows Explorer, use the :code:`explorer.exe .`

command (do not forget the final dot!).

.. image:: img/wsl_tutorial/wsl_integration.png

   :scale: 50%

--------

Compiling LAMMPS

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

You now have a fully functioning Ubuntu installation and can follow most

guides to install LAMMPS on a Linux system. Here are some of the essential

steps to follow:

Install prerequisite packages

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

Before we can begin, we need to download the necessary compiler toolchain and

libraries to compile LAMMPS. In our Ubuntu-based Linux installation, we will

use the :code:`apt` package manager to install additional packages.

First, upgrade all existing packages using :code:`apt update` and :code:`apt upgrade`.

.. code-block:: bash

   sudo apt update

   sudo apt upgrade -y

Next, install the following packages with :code:`apt install`:

.. code-block:: bash

   sudo apt install -y cmake build-essential ccache gfortran openmpi-bin libopenmpi-dev \

                       libfftw3-dev libjpeg-dev libpng-dev python3-dev python3-pip \

                       python3-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev \

                       hdf5-tools

Download LAMMPS

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

Obtain a copy of the LAMMPS source code and go into it using the :code:`cd` command.

Option 1: Download a LAMMPS tarball using wget

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

.. code-block:: bash

   wget https://github.com/lammps/lammps/archive/stable_3Mar2020.tar.gz

   tar xvzf stable_3Mar2020.tar.gz

   cd lammps

Option 2: Download a LAMMPS development version from GitHub

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

.. code-block:: bash

   git clone --depth=1 https://github.com/lammps/lammps.git

   cd lammps

Configure and Compile LAMMPS with CMake

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

A beginner-friendly way to compile LAMMPS is to use CMake. Create a :code:`build`

directory to compile LAMMPS and move into it. This directory will store the

build configuration and any binaries generated during compilation.

.. code-block:: bash

   mkdir build

   cd build

There are countless ways to compile LAMMPS. It is beyond the scope of this

tutorial. If you want to find out more about what can be enabled, please

consult the extensive `documentation <https://lammps.sandia.gov/doc/Build_cmake.html>`_.

To compile a minimal version of LAMMPS, we're going to use a preset.

Presets are a way to specify a collection of CMake options using a file.

.. code-block:: bash

   cmake ../cmake/presets/minimal.cmake ../cmake

This command configures the build and generates the necessary Makefiles. To compile the binary, run the make command.

.. code-block:: bash

   make -j 4

The :code:`-j` option specifies how many parallel processes will perform the

compilation. This option can significantly speed up compilation times. Use a

number that corresponds to the number of processors in your system.

After the compilation completes successfully, you will have an executable

called :code:`lmp` in the :code:`build` directory.

.. image:: img/wsl_tutorial/compilation_result.png

   :scale: 50%

Please take note of the absolute path of your :code:`build` directory. You will

need to know the location to execute the LAMMPS binary later.

One way of getting the absolute path of the current directory is through the

:code:`$PWD` variable:

.. code-block:: bash

   # prints out the current value of the PWD variable

   echo $PWD

Let us save this value in a temporary variable :code:`LAMMPS_BUILD_DIR` for future use:

.. code-block:: bash

   LAMMPS_BUILD_DIR=$PWD

The full path of the LAMMPS binary then is :code:`$LAMMPS_BUILD_DIR/lmp`.

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

Running an example script

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

Now that we have a LAMMPS binary, we will run a script from the examples folder.

Switch into the :code:`examples/melt` folder:

.. code-block::

   cd ../examples/melt

To run this example in serial, use the following command line:

.. code-block::

   $LAMMPS_BUILD_DIR/lmp -in in.melt

To run the same script in parallel using MPI with 4 processes, do the following:

.. code-block:: bash

   mpirun -np 4 $LAMMPS_BUILD_DIR/lmp -in in.melt

If you run LAMMPS for the first time, the Windows Firewall might prompt you

to confirm access. LAMMPS is accessing the network stack to enable parallel

computation. Allow the access.

.. image:: img/wsl_tutorial/windows_firewall.png

   :scale: 75%

In either serial or MPI case, LAMMPS executes and will output something similar to this:

.. code-block::

   LAMMPS (30 Jun 2020)

   ...

   ...

   ...

   Total # of neighbors = 151513

   Ave neighs/atom = 37.878250

   Neighbor list builds = 12

   Dangerous builds not checked

   Total wall time: 0:00:00

**Congratulations! You've successfully compiled and executed LAMMPS on WSL!**

Final steps

===========

It is cumbersome to always specify the path of your LAMMPS binary. You can

avoid this by adding the absolute path of your :code:`build` directory to your PATH

environment variable.

.. code-block:: bash

   export PATH=$LAMMPS_BUILD_DIR:$PATH

You can then run LAMMPS input scripts like this:

.. code-block:: bash

   lmp -in in.melt

or

.. code-block:: bash

   mpirun -np 4 lmp -in in.melt

.. note::

   The value of this :code:`PATH` variable will disappear once you close your

   console window. To persist this setting edit the :code:`$HOME/.bashrc` file using your

   favorite text editor and add this line:

   .. code-block:: bash

      export PATH=/full/path/to/your/lammps/build:$PATH

   **Example:**

   If the LAMMPS executable `lmp` has the following absolute path:

   .. code-block:: bash

      /home/<USERNAME>/lammps/build/lmp

   the :code:`PATH` variable should be:

   .. code-block:: bash

      export PATH=/home/<USERNAME>/lammps/build:$PATH

   Once set up, all your Ubuntu consoles will always have access to your :code:`lmp`

   binary without having to specify its location.

Conclusion

==========

I hope this gives you good overview on how to start compiling and running LAMMPS on

Windows. WSL makes preparing and running scripts on Windows a much better

experience.

If you are completely new to Linux, I highly recommend investing some time in

studying Linux online tutorials. E.g., tutorials about Bash Shell and Basic

Unix commands (e.g., `Linux Journey <https://linuxjourney.com/>`_). Acquiring

these skills will make you much more productive in this environment.

.. seealso::

   * `Windows Subsystem for Linux Documentation <https://docs.microsoft.com/en-us/windows/wsl/>`_