Working on Linux#

As you participate in this lab exercise, you must have at least a basic knowledge of working with a Linux computer. This chapter shows you the basic commands to get along with your computational environment. First of all, you will be provided with a username and a password. This represents your user account for the whole lab course and all the data you produce is available with this information.


Some of the keyboard shortcuts in this chapter are targeted at the setup of the CIP Pool computers in the Mulliken Center for Theoretical Chemistry and might not work as expected for you.

In case you use KDE, everything will probably work just fine, if you use another OS or window manager commands might differ slightly.


The first thing you will see after booting the computer is the login-screen.

Dependent on the Linux version you are using this screen may look slightly different. After you typed in your username and password you press the <Return> key and the graphical desktop will be loaded. All further actions will take place in this environment. The next and certainly most important thing is to access the Linux command line. This is usually done by starting a terminal-emulator, which is called shell or terminal. On the machines you are using there should be a quick start icon directly on the desktop. By clicking on this icon, a window is opened which allows you to communicate with the PC in a command-line mode.

Shell in a nutshell#

After executing the terminal-emulator you will end up with a window, which looks similar to the following image:

ehlert@c01:~> pwd
ehlert@c01:~> ls
Desktop     Music      QCII
Documents   Pictures   Templates
Downloads   Public     Videos
ehlert@c01:~> cd QCII

On the left, you can see the so-called prompt. Depending on the default settings of your system it provides you with various information. In a standard configuration, it will show: username@hostname:~>, where username is your username, hostname is the name of the computer and the tilde (~) shows that you are currently located in your home directory (/home/username). The Linux file structure follows the Filesystem Hierarchy Standard, which ensures a similar file structure on every version of Linux you can get. As you work with the system you will rapidly gain experience with the different directories and their purposes. For now, you should know that you are in your home directory which is located at /home/username and is abbreviated by ~.

With your user account you have the power to create, edit, and delete files in your home directory at will. But with great power comes great responsibility. You have to be careful with the commands you execute when you delete or overwrite a file it is gone for good. With that in mind, we can now start with the first couple of commands. To see exactly which directory you are in, type pwd (print working directory) and press <Return>. Since you are in your home directory, this will print the path to that home directory to the screen. Note that all input in the terminal is case-sensitive.

ehlert@c01:~> pwd

Next thing we want to know is what is inside our current location, for this we use the command ls, short for list:

ehlert@c01:~> ls
Desktop     Music      QCII
Documents   Pictures   Templates
Downloads   Public     Videos

We can add options to the ls command like -l to use the use a long listing format:

ehlert@c01:~> ls -l
total 574500
drwxr-xr-x  2 ehlert thch      4096 Jun  7  2018 Desktop
drwxr-xr-x  2 ehlert thch      4096 Jun  7  2018 Documents
drwxr-xr-x  2 ehlert thch      4096 Jun  7  2018 Downloads
drwxr-xr-x  2 ehlert thch      4096 Jun  7  2018 Music
drwxr-xr-x  2 ehlert thch      4096 Jun  7  2018 Pictures
drwxr-xr-x  2 ehlert thch      4096 Jun  7  2018 Public
drwxr-xr-x  4 ehlert thch      4096 Jan 14 09:09 QCII
drwxr-xr-x  2 ehlert thch      4096 Jun  7  2018 Templates
drwxr-xr-x  2 ehlert thch      4096 Jun  7  2018 Videos

Alternatively we can provide ls with a path, it will then list all the files within this directory

ehlert@c01:~> ls QCII
tutorial   scf

Of course we can also combine options and paths for ls.

You might wonder what a path is, we will go into more detail above them now as they are important for working with Linux. Whenever we refer to a file or a directory on the commandline we are in fact referring to its path. A path is identifying a particular file or directory on the system. Your filesystem starts at the root / and can be referenced absolutely from this root or relative from your current working directory. Every directory has at least two links to other directories, to itself . (dot) and to its parent .. (dotdot), which can be used to build paths to reference to any file or directory on your system.

Up to now we only looked around, but we can also change the directory, which is done by the command cd, short for change directory.

ehlert@c01:~> cd QCII
ehlert@c01:~/QCII> cd .
ehlert@c01:~/QCII> cd ../..
ehlert@c01:/home> cd -
ehlert@c01:~/QCII> cd

What did just happen?

  1. We changed to the QCII directory. Our prompt helpfully reports that we are now in the QCII directory, so usually there is no need to use pwd.

  2. Next we change to the directory itself using its dot link, and we stay in the same directory as expected.

  3. Now we change to the parent directory of the QCII parent directory, which is the parent directory of our home directory. You can easily chain links together using the slash character /.

  4. In case a change directory brings you to the wrong place you can always go back to the last directory you visited by cd -. The absolute path of the directory is also printed so we can be sure to be in the right place.

  5. To go back to your home directory use cd without an argument.

We differenciated files and directories above, which is not quite true, in Linux everything is a file, also a directory, even your keyboard is a file (one which is only read from), your monitor is also a file (one which is only written to). It will not affect us when working with Linux but it is helps to keep it in mind when trying to understand how Linux manages files and directories.

A standard set of commands is shown in the following table:




print the working directory


lists the files in the current directory

cd <name>

change to the directory with <name>

cd ..

change to the parent directory

cp <old> <new>

copy file <old> to <new>

cp -r <old> <new>

copy directory <old> to <new>

mv <old> <new>

move (rename) file/directory

rm <name>

remove file with <name>

rm -r <name>

remove directory recursively (caution!)

mkdir <name>

make a new directory with <name>

rmdir <name>

remove (empty) directory with <name>

This is only a very basic list of commands available and some of them have a huge variety of options that can not be listed here, and will hardly concern you. For all options the program can be started with <command> --help and a complete summary can be found in its manual page by man <command>.

Exercise 1

To get familiar with the shell try to achieve the following task

  1. change to the QCII directory

  2. find or create the tutorial directory in QCII

  3. rename the tutorial directory to shell tutorial

  4. change to the newly created directory

Solutions 1

A sequence of this command would achieve the wished results.

username@hostname:~> cd QCII
username@hostname:~/QCII> ls tutorial
username@hostname:~/QCII> mv tutorial shell tutorial
mv: cannot move 'tutorial' to a subdirectory of itself, 'tutorial/tutorial'
mv: cannot stat 'shell': No such file or directory
username@hostname:~/QCII> mv tutorial 'shell tutorial'
username@hostname:~/QCII> cd shell\ tutorial
username@hostname:~/QCII/shell tutorial>

Note that you have to escape the space in shell tutorial in some way.


To access and edit any text file in Linux you will need an editor. A huge variety of editors exist and your difficult task is to pick the one you are most comfortable with. We introduce the most common ones in this chapter but feel free to work with the editor that fits you the best.


atom is a rather heavyweight but easy-to-use editor, which is built on-top of the electron framework and has comparable capabilities to a web browser. It is available for Linux, macOS and Windows. Since we are dealing here with electrons and atoms the choice of programs could not have been better, unfortunately, they do not know much about quantum chemistry. For you can work entirely in atom, but you need some extension which might already be installed with your version of atom. If not install language-fortran, build, build-make and terminal-tab at the setting menu <ctrl>-<,> under install. atom can be easily extended to a complete integrated development environment, but we will assume you are working with a vanilla version including the four additional packages here.

Start atom by using <alt>-<F2> and typing atom in the quick launch bar or searching the start menu for atom.

New atom instance

Having started a new instance of atom you either have already an empty file opened or you can open a new file by <ctrl>-<n>, save the file with <ctrl>-<s> by creating a new directory and giving the file a name there, if you name the file hello.f90 it will be automatically identified as Fortran source code.

Always save your files

You can start a shell by hitting <ctrl>-<shft>-<p> and typing terminal in the quick launcher of atom the shell can be used for all commands you previously learned.

Quicklaunch terminal


If you are using atom in Windows and have installed WSL, you can start a Unix shell by typing wsl or bash in the command line of the terminal you just opened in atom.

Later you can use it to compile and execute your programs without leaving your editor. For example, we write a simple Fortran program to print a line to the screen, save it and compile it using gfortran in our shell inside atom.

Running gfortran from atom


We usually prefer to use vim which is a very powerful and lightweight editor once you have mastered the initial steep learning curve. It has the advantage of being installed by default on almost any Linux machine and is even fully usable without a graphical user interface.

However, getting past the initial learning curve can take the better part of a month, but having truly mastered vim usually results in a huge performance gain when developing. We encourage you to pick up vim instead of atom.

To get started with vim open a new terminal (type <alt>-<F2> for the quick launch menu, then type konsole or search for it in the menu) and type vimtutor. This will launch an instance of vim with an extensive introduction for using it, follow the instructions until you feel confident navigating and editing files with vim.


Don’t read past this note without finishing vimtutor!

To make working with vim easier for you, we provide this .vimrc for you:

" Defaults for new vim users.
source $VIMRUNTIME/defaults.vim
" Ignore this filetypes in the wildmenu
set wildignore=*.o,*~,*.pyc,*.mod
" Make search case insensitive, but only as long as it contains only lowercase
set ignorecase
set smartcase
" Automatic indentation
set autoindent
set smartindent
set tabstop=4
set shiftwidth=4
set smarttab
set expandtab
" Fortran specific options
let fortran_do_enddo=1
let fortran_free_source=1

In case it is not yet in your .vimrc we recommend copying, if you are not happy with something we put in here, feel free to modify or replace it, you can also add new configurations if you like.

After you have covered the basics, there are some tricks you might find useful.


We recommend working with a single instance of vim in one terminal, if used right vim can provide all functions from your file navigator and terminal.

  1. Open your current working directories with vim . and you will find yourself in the netrw file navigator.

  2. Navigate to a file you would like to open and hit <Enter>, it will be opened in the same vim instance, to get back type :E in normal mode and find yourself back in netrw.

  3. To open a new window type <ctrl>-w n, you can close the window again with <ctrl>-w q or by typing :q as usual.

  4. To open a second window you can split your vim window by using <ctrl>-w v (for vertical splitting) or <ctrl>-w s (for horizontal splitting) to have two windows with the same file which can be used independently.


If your vim instance freeze, you hit <ctrl>-s by accident, which tells the hosting terminal to freeze, unfreeze it with <ctrl>-q.

  1. If you have your mouse enabled for vim you can jump between windows by clicking into another window, the faster way is to use <ctrl>-w w to go to the next window.

Make yourself familiar with navigation between multiple windows by creating, closing and jumping between multiple windows. You can yank and paste content between the windows that way, which allows seamless transfer between different files.

  1. Now go in one of the windows back to netrw, we want to create a new directory without using :!mkdir ..., type d in normal mode in your netrw instance and you should be prompted to provide a name.

  2. You can delete it again with D, do so by moving your cursor over the file or directory and press D, then accept your choice in the prompt.

  3. Now we want a new file, the easiest way would be :e ..., but this path has to be relative from the working directory we started our vim instance in, so we use netrw instead and type % which prompts as to provide a name and opens the new file afterward in a new vim window.

Let’s open a new file hello.f90 and enter

1program hello
2   implicit none
3   write(*, '(a)') "My first Fortran program"
4end program hello


In case the syntax highlighting looks strange, vim is trying to use Fortran 77 highlighting, add let fortran_free_source=1 to your .vimrc to get the correct Fortran 90 highlighting and restart vim for it to take effect.

After saving the file, compile and run it by typing :!gfortran % && ./a.out, you should see something like this printout in your terminal:

My first Fortran program

Press ENTER or type command to continue

The first line is from your program, the second one is produced by vim.


To switch between your terminal and vim use <ctrl>-z to stop vim and get it back from the terminal by using the command fg.

At this point, you should be ready to use vim in production, happy coding.