⚛️ Laboratory Work: Computational Methods with Quantum ESPRESSO

Course: Computational Methods for Atomistic Simulations
Authors: Khasan Akhmadiev, Alexander Kvashnin
Purpose: This repository contains laboratory assignments for the course, focusing on calculating phonon / electronic properties of materials using the Quantum ESPRESSO (QE) package.

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⚙️ Setup and Execution

This project is primarily designed for running calculations on a remote server.

1. Repository Cloning

1. Create a working directory on the server.
2. Clone the repository:

   git clone https://github.com/hasaki77/QE_Laboratory_Work.git
   cd QE_Laboratory_Work

2. Environment Setup (Conda)

An isolated environment is required to run the Jupyter Notebooks.

1. Install the necessary packages using the dependency file (environment.yml):

   conda env create -f environment.yml
   conda activate lab_env
   pip install git+https://github.com/Griffin-Group/pymatgen-io-espresso

2. Activating mpirun Before executing any calculation, ensure the QE environment variables are correctly sourced. Check, that MPI is working:

   mpirun --version

3. Running Lab Assignments

1. Connect to the server using VSCode Remote-SSH (recommended) or open a Jupyter Notebook server session.
2. Open the lab assignment file (e.g., 1_Structure_Optimization.ipynb).
3. Inside the Notebook, select the kernel lab_env.
4. Run all cells to confirm functionality.

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📌 Lab Assignments and Objectives

Each lab assignment is presented as a separate Jupyter Notebook, which includes a theoretical introduction, calculation code, and specific tasks.

No.	Assignment Title	Primary Objective	File Link
1	Structure Optimization	Optimize cut-off energy and k-points parameters, followed by structure relaxation.	1_Structure_Optimization.ipynb
2	Phonon & Electronic Properties	Calculate phonon/electronic Density of States (DOS) and band structures.	2_Electron_Phonon_props.ipynb
3	MLIP Training	Implement Molecular Dynamics to generate structures used for training a Machine Learning Interatomic Potential (MLIP).	3_MLIP_calculation.ipynb

🔬 Project Assignment

In addition to the labs, students must select a second structure (of their own choice) to implement the Final Project.

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💻 Recommended Software for Connection

Category	Software	Link	Purpose
SSH Client	PuTTY / Built-in Terminal	putty.org	Remote connection to the server.
Code Editor	VSCode with Remote-SSH	code.visualstudio.com	Code editing and running Jupyter Notebooks.
SFTP Client	WinSCP / FileZilla	winscp.net	Managing files between local machine and server.

Good luck with your calculations! 🍀