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Efficient materials modelling on HPC with QUANTUM ESPRESSO, SIESTA and Yambo (Online)

11-15 March 2024, 09:00–13:00 CET

Overview

This workshop will give a broad overview of important fundamental concepts for molecular and materials modelling on HPC, with a focus on three of the most modern codes for electronic structure calculations (QUANTUM ESPRESSO, Yambo and SIESTA). Participants will put their new knowledge to the test on the Leonardo EuroHPC JU supercomputer (https://leonardo-supercomputer.cineca.eu/hpc-system/) with theory sections and practical demonstrations and hands-on exercises.

In recent years, computing technologies underlying materials modelling and electronic structure calculation have evolved rapidly. High-performance computing (HPC) is transitioning from petascale to exascale, while individual compute nodes are increasingly based on heterogeneous architectures that every year become more diversified due to different vendor choices. In this environment, electronic structure codes also have to evolve fast in order to adapt to new hardware facilities.

Nowadays, state-of-the-art electronic structure codes based on modern density functional theory (DFT) methods allow treating realistic molecular systems with a very high accuracy. However, due to the increased complexity of the codes, users need some extra skills in order to fully exploit their potential.

The applications

QUANTUM ESPRESSO (https://www.quantum-espresso.org/) is one of the most popular suites of computer codes for electronic-structure calculations and materials modelling at the nanoscale, based on density-functional theory, plane waves, and pseudopotentials. It is able to predict and give fundamental insights about many properties of materials, molecular systems, micro and nanodevices, biological systems, in many fields, providing a huge amount of data for data-driven science applications.

SIESTA (http://www.max-centre.eu/codes-max/siesta) is a pseudopotential-based DFT software whose strength lies in its use of atomic-like strictly-localised basis sets: the use of a "good first approximation" to the full problem decreases the number of basis functions needed to achieve a given accuracy, and the finite support of the orbitals leads to sparsity in the Hamiltonian and overlap matrices, thus enabling the use of reduced-scaling methods. The functionalities of SIESTA include, amongst others, the calculation of energies and forces, molecular-dynamics simulations, band structures, densities of states, spin-orbit couplings, van der Waals functionals, DFT+U for correlated systems, real-time TDDFT, and non-equilibrium calculations with TranSIESTA.

YAMBO (http://www.yambo-code.eu/) is an open-source code implementing first-principles methods based on Green’s function (GF) theory to describe excited-state properties of realistic materials. These methods include the GW approximation, the Bethe Salpeter equation, nonequilibrium GF (NEGF) and TDDFT, allowing for the prediction of accurate quasiparticle energies (e.g. ARPES band structures), linear and non-linear optical properties, capturing the physics of excitons, plasmons, and magnons. It is also possible to calculate temperature-dependent electronic and optical properties via electron-phonon coupling and nonequilibrium and non-linear optical properties via NEGF real-time simulations (pump-probe experiments, etc).

What you will learn

In this workshop, participants will learn how to launch the most common types of calculations (e.g. scf, phonons, quasi-particle energies, time-dependent properties) using Quantum ESPRESSO, Yambo and SIESTA, how to prepare input files and how to read output files in order to extract the desired properties.

You will discuss efficient exploitation of HPC resources, with particular emphasis on how to use the different schemes of data distribution (e.g. plane waves, pools, images) in combination with the different parallelization and acceleration schemes (MPI, OpenMP, GPU-offload) available in Quantum ESPRESSO, SIESTA and Yambo.

Prerequisites

This workshop is for researchers and engineers who already have some previous experience with materials modelling and electronic structure calculations:

  • Basic familiarity with density functional theory (DFT), self-consistent field (SCF) calculations and plane wave basis sets is desirable as the workshop will not cover the fundamental theory of these topics.
  • Basic familiarity with working in a Linux environment and some experience with working on an HPC system is needed to participate in the hands-on exercises.

Disclaimer

Due to EuroCC2 regulations, we cannot except generic or private email addresses. Please use your official university or company email address.

This training is intended for users that live and work in the European Union or a country associated with Horizon 2020. You can read more about the countries associated with Horizon2020 here https://ec.europa.eu/info/research-and-innovation/statistics/framework-programme-facts-and-figures/horizon-2020-country-profiles_e


Lecturers

  • Andrea Ferretti, CNR-NANO
  • Daniele Varsano, CNR-NANO
  • Pietro Delugas, SISSA
  • Ivan Carnimeo, SISSA
  • Oscar Baseggio, SISSA
  • P. Giannozzi
  • Iurii Timrov, EPFL CH
  • Laura Bellentani, CINECA
  • Tommaso Gorni, CINECA
  • D. Sangalli
  • A. Guandalini
  • M. D’Alessio
  • Ignacio Alliati, Univ. Bellfast
  • Emilio Artacho, University of Cambridge and CIC nanoGUNE
  • Catalina Coll, Catalan Institute of Nanoscience and Nanotechnology
  • José Mª Escartín, Catalan Institute of Nanoscience and Nanotechnology
  • Roberta Farris, Catalan Institute of Nanoscience and Nanotechnology
  • Ernane de Freitas, Catalan Institute of Nanoscience and Nanotechnology
  • Alberto García, ICMAB-CSIC
  • Nick Papior, Technical University of Denmark
  • Federico Pedron, Catalan Institute of Nanoscience and Nanotechnology
  • Miguel Pruneda, ICNN-CSIC José Ángel Silva, IMDEA Nanociencia

Agenda

Monday, March 11th

Time (CET)Topic
09:00-09:15Welcome and introduction to ENCCS
09:15-09:30Introduction to Max-CoE and MaX flagship codes
09:30-10:10Overview of the QE suite of codes and main features
10:10-10:25Coffee break
10:25-13:00PWSCF for HPC and GPU

Tuesday, March 12th

Time (CET)Topic
09:00-09:45Introduction to Density Functional Perturbation Theory
09:45-10:15Introduction to Time Dependent Density Functional Perturbation Theory
10:15-10:30Coffee break
10:30-13:00Phonons and time dependent properties on HPC and GPU

Wednesday, March 13th

Time (CET)Topic
09:00-09:45SIESTA basics
09:45-10:30A first contact with SIESTA: inputs, execution and outputs
10:30-10:45Break
10:45-11:30Convergence (K points, Mesh, Mixing)
11:30-12.00Basis sets
12:00-13:00Basis set optimization

Thursday, March 14th

Time (CET)Topic
09:00-10:00Moving atoms: geometry optimisation and beyond
10:00-11:00Analysis tools
11:00-11:15Break
11:15-11:45Features available in SIESTA: spin-orbit couplings, TranSIESTA, and others
11:45-13:00Pushing the boundaries of SIESTA: accelerated and massively parallel solvers

Friday, March 15th

Time (CET)Topic
09:00-09:20Overview of the Yambo code and its main features and performance
09:20-10:00Introduction to the GW approximation
10:00-10:20Coffee break
10:20-13:00Hands-on tutorial: A guided tour through GW simulations
(convergence, algorithms, parallel usage)

ENCCS Lessons

The previous similar instance of Efficient Materials Modelling can be found at our page with previous lesson materials.

Free