Merge pull request #605 from rbberger/bash_on_windows

Adds tutorial for using LAMMPS in Bash on Windows

doc/src/tutorial_bash_on_windows.txt

+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+Using LAMMPS with Bash on Windows :h3
+[written by Richard Berger]
+
+:line
+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.
+
+Installing Bash on Windows :h4
+
+Prerequisites :h5
+
+Windows 10 (64bit only)
+Latest updates installed :ul
+
+Enable developer mode :h5
+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,JPG/bow_tutorial_01.png)
+:image(JPG/bow_tutorial_02_small.png,JPG/bow_tutorial_02.png)
+:image(JPG/bow_tutorial_03_small.png,JPG/bow_tutorial_03.png)
+
+Install Windows Subsystem for Linux :h5
+
+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,JPG/bow_tutorial_04.png)
+:image(JPG/bow_tutorial_05.png,JPG/bow_tutorial_05.png)
+
+Install Bash for Windows :h5
+
+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)
+
+:line
+
+Compiling LAMMPS in Bash on Windows :h4
+
+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 :h5
+
+First upgrade all existing packages using
+
+sudo apt update
+sudo apt upgrade -y :pre
+
+Next install the following packages, which include compilers and libraries
+needed for various LAMMPS features:
+
+sudo apt install -y build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng12-dev python-dev python-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tools :pre
+
+Files in Ubuntu on Windows :h5
+
+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 :h5
+
+Obtain a copy of the LAMMPS code and go into it using "cd"
+
+Option 1: Downloading LAMMPS tarball using wget :h6
+
+wget http://lammps.sandia.gov/tars/lammps-stable.tar.gz
+tar xvzf lammps-stable.tar.gz
+cd lammps-31Mar17 :pre
+
+Option 2: Obtaining LAMMPS code from GitHub :h6
+
+git clone https://github.com/lammps/lammps.git
+cd lammps :pre
+
+Compiling LAMMPS :h5
+
+At this point you can compile LAMMPS like on Ubuntu Linux.
+
+Compiling serial version :h6
+
+cd src/
+make -j 4 serial :pre
+
+This will create an executable called lmp_serial in the src/ directory
+
+Compiling MPI version :h6
+
+cd src/
+make -j 4 mpi :pre
+
+This will create an executable called lmp_mpi in the src/ directory
+
+:line
+
+Finally, please note the absolute path of your src folder. You can get this using
+
+pwd :pre
+
+or
+
+echo $PWD :pre
+
+To run any examples you need the location of the executable. For now, let us
+save this location in a temporary variable
+
+LAMMPS_DIR=$PWD :pre
+
+:line
+
+Running an example script :h5
+
+Once compiled you can execute some of the LAMMPS examples. Switch into the
+examples/melt folder
+
+cd ../examples/melt :pre
+
+The full path of the serial executable is $LAMMPS_DIR/lmp_serial, while the mpi
+version is $LAMMPS_DIR/lmp_mpi. You can run the melt example with either
+version as follows:
+
+$LAMMPS_DIR/lmp_serial -in in.melt :pre
+
+or
+
+mpirun -np 4 $LAMMPS_DIR/lmp_mpi -in in.melt :pre
+
+Note the use of our variable $LAMMPS_DIR, which expands into the full path of
+the LAMMPS src folder we saved earlier.
+
+Adding your executable directory to your PATH :h6
+
+You can avoid having to type the full path of your LAMMPS binary by adding its
+parent folder to the PATH environment variable as follows:
+
+export PATH=$LAMMPS_DIR:$PATH :pre
+
+Input scripts can then be run like this:
+
+lmp_serial -in in.melt :pre
+
+or
+
+mpirun -np 4 lmp_mpi -in in.melt :pre
+
+However, this PATH variable will not persist if you close your bash window.
+To persist this setting edit the $HOME/.bashrc file using your favorite editor
+and add this line
+
+export PATH=/full/path/to/your/lammps/src:$PATH :pre
+
+[Example:]
+
+For an executable lmp_serial with a full path
+
+/home/richard/lammps/src/lmp_serial :pre
+
+the PATH variable should be
+
+export PATH=/home/richard/lammps/src:$PATH :pre
+
+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)

doc/src/tutorials.txt

@@ -8,6 +8,7 @@ Tutorials :h1
    tutorial_drude
    tutorial_github
    tutorial_pylammps
+   tutorial_bash_on_windows
    body
    manifolds