2. Productivity tools: Linux and JupyterLab¶

2.1. Ubuntu¶

Ubuntu is a popular, free, and open-source operating system based on the Linux kernel.

2.1.1. How to download and install Ubuntu¶

Step 1: Download Ubuntu ISO¶

• Go to the official Ubuntu website: https://ubuntu.com/download
• Choose the version you want (e.g., Ubuntu Desktop LTS or Ubuntu Server)
• Click Download to get the .iso file

Step 2: Create a Bootable USB Drive¶

• A USB stick with at least 8 GB capacity
• Bootable USB Live by a tool like Rufus (for Windows) or balenaEtcher (for Mac/Linux)

Step 3: Boot From USB¶

1. Insert the bootable USB into the target computer
2. Restart the computer
3. Enter BIOS/UEFI (usually by pressing F2, F12, DEL, or ESC)
4. Set the USB drive as the primary boot device
5. Save and exit

Step 4: Install Ubuntu¶

1. Choose "Install Ubuntu" when the menu appears
2. Select your language, keyboard layout, and other preferences
3. Choose installation type:
   • Erase disk and install Ubuntu
   • Install alongside existing OS
   • Something else (for custom partitions)
4. Follow prompts to set username, password, and location
5. Wait for installation to complete
6. Reboot when prompted, remove the USB

Step 5: Post-Installation (Optional)¶

• Update system:

sudo apt update && sudo apt upgrade -y

• Install Quantum ESPRESSO: See 1.5.1 in Lecture 1: Introduction to DFT with QE

2.1.2. Basic Ubuntu (Linux) commands¶

Command	Description	Example
ls	List directory contents	ls -la
cd	Change directory	cd /home/user/Documents
pwd	Print working directory	pwd
mkdir	Create a new directory	mkdir new_folder
rm	Remove files or directories	rm file.txt
rmdir	Remove empty directory	rmdir empty_folder
cp	Copy files or directories	cp file1.txt file2.txt
mv	Move or rename files	mv old.txt new.txt
touch	Create an empty file	touch file.txt
nano / vim	Edit files with a text editor	nano file.txt
cat	Display file contents	cat file.txt
sudo	Run command as superuser	sudo apt update
apt	Package manager for Debian/Ubuntu	sudo apt install curl
man	Display manual for a command	man ls
chmod	Change file permissions	chmod +x script.sh
chown	Change file ownership	chown user:user file.txt
df	Show disk space usage	df -h
top	Show real-time system processes	top
ps	Show running processes	ps aux
kill	Terminate a process by PID	kill 1234

2.1.3. Basic Quantum ESPRESSO (QE) commands¶

Command	Description	Example
pw.x	Runs the Plane-Wave Self-Consistent Field (SCF) code	pw.x < scf.in > scf.out
dos.x	Computes Density of States	dos.x < dos.in > dos.out
projwfc.x	Projects wavefunctions (for PDOS)	projwfc.x < projwfc.in > projwfc.out
bands.x	Computes band structure from saved data	bands.x < bands.in > bands.out
ph.x	Runs phonon calculations	ph.x < ph.in > ph.out
q2r.x	Converts dynamical matrices from q to real space	q2r.x < q2r.in > q2r.out
matdyn.x	Calculates phonon dispersion and DOS	matdyn.x < matdyn.in > matdyn.out
pp.x	Post-processing (e.g., charge density visualization)	pp.x < pp.in > pp.out
mpirun -np N pw.x	Run SCF with MPI on N cores	mpirun -np 8 pw.x < scf.in > scf.out
pw.x -in input.in	Alternate input format (no I/O redirection)	pw.x -in scf.in

2.2. JupyterLab on Ubuntu¶

2.2.1. What is JupyterLab?¶

JupyterLab is a next-generation web-based interactive development environment for notebooks, code, and data. It's an evolution of the classic Jupyter Notebook, with support for:

• Multiple documents and editors (notebooks, terminals, text files, etc.)
• Drag-and-drop interface
• Rich extensions and themes

Great for data science, machine learning, scientific computing, and research.

2.2.3. How to Install JupyterLab on Ubuntu¶

Step 1: Update Your System¶

$ sudo apt update && sudo apt upgrade -y

Step 2: Install Python and Pip¶

$ sudo apt install python3 python3-pip -y

Step 4: Install JupyterLab¶

$ pip install jupyterlab

Step 5: Additional Python scientific libraries¶

$ pip install numpy scipy sympy matplotlib

• numpy: numerical computing with arrays
• scipy: scientific computing, linear algebra, optimization, etc.
• sympy: symbolic mathematics (like algebra, calculus, equation solving)
• matplotlib: plotting and data visualization

Step 6 (optional): JupyterLab extensions¶

$ pip install nodejs

• nodejs: an open-source, cross-platform environment for running JavaScript applications. Some extensions might require a rebuild of JupyterLab upon installation. This rebuild process relies on Node.js.

2.2.4. How to Use JupyterLab¶

Step 1: Start JupyterLab¶

$ jupyter lab

• This will launch JupyterLab in your browser at http://localhost:8888
• A token will be printed in the terminal if not previously configured

Step 2: Create Notebooks or Scripts¶

• Use the launcher interface to open:
  • Python notebooks
  • Markdown files
  • Terminal sessions
  • Text/code editors

Step 3: Stop JupyterLab¶

• Press Ctrl+C in the terminal where it's running
• Type y and press Enter to confirm shutdown

2.3. JupyterLab on Visual Studio Code (VS Code)¶

2.3.1. What is Visual Studio Code (VS Code)?¶

Visual Studio Code (VS Code) is a free, open-source, and lightweight code editor developed by Microsoft. It is widely used by developers for writing, editing, debugging, and deploying code across many programming languages and platforms.

2.3.2: Install Visual Studio Code on Ubuntu¶

Method 1: Install via apt (Recommended)¶

$ sudo apt update
$ sudo apt install wget gpg -y
$ wget -qO- https://packages.microsoft.com/keys/microsoft.asc | gpg --dearmor > packages.microsoft.gpg
$ sudo install -o root -g root -m 644 packages.microsoft.gpg /usr/share/keyrings/
$ sudo sh -c 'echo "deb [arch=amd64 signed-by=/usr/share/keyrings/packages.microsoft.gpg] \
https://packages.microsoft.com/repos/code stable main" > /etc/apt/sources.list.d/vscode.list'

$ sudo apt update
$ sudo apt install code

Method 2: Install from .deb File¶

• Download .deb from: https://code.visualstudio.com/
• Install with:

$ sudo dpkg -i code_*.deb
$ sudo apt --fix-broken install

2.3.3: Install Jupyter Extension in VS Code¶

1. Open VS Code
2. Go to the Extensions tab (or press Ctrl+Shift+X)
3. Search for "Jupyter" (by Microsoft)
4. Click Install

2.3.4. Run Jupyter Notebooks in VS Code¶

Option 1: Create a New Notebook¶

• Press Ctrl+Shift+P, search Jupyter: Create New Blank Notebook
• Choose a kernel (Python 3, etc.)

Option 2: Open an Existing .ipynb File¶

• File → Open File → select your .ipynb notebook
• You’ll see interactive cells inside VS Code

1.6. Exercise¶

• Practice with Linux command line and JupyterLab on your PC.

1.7. Dive deeper¶

• Level 1: Read Chapter 6 of "Quantum ESPRESSO for Solid State Physics" book for Linux commands.

• Level 2: Install and run JupyterLab on VSCode.