Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo

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, some extra skills are required from users in order to fully exploit their potential.

This training material gives 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, SIESTA and Yambo). Theory sections are interleaved with practical demonstrations and hands-on exercises.

QUANTUM ESPRESSO 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 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 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).

MAX (MAterials design at the eXascale) is a European Centre of Excellence which enables materials modelling, simulations, discovery and design at the frontiers of the current and future High-Performance Computing (HPC), High Throughput Computing (HTC) and data analytics technologies. MaX’s challenge lies in bringing the most successful and widely used open-source, community codes in quantum simulations of materials towards exascale and extreme scaling performance and make them available for a large and growing base of researchers in the materials’ domain.

Prerequisites

  • Some 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.

  • 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.

Who is the course for?

This workshop is aimed towards researchers and engineers who already have some previous experience with materials modelling and electronic structure calculations.

Days 1 and 2 - Quantum ESPRESSO

Days 3 and 4 - Siesta

Day 5 - Yambo

Reference

About

About the course

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 QE, SIESTA and Yambo, how to prepare input files and how to read output files in order to extract the desired properties.

Best practices for efficient exploitation of HPC resources will be discussed. On the QE days, there will be 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. Regarding SIESTA, participants will learn about its algorithmic efficiency, and they will be able to explore its accelerated and massively parallel solvers.

Schedule

Day 1, QUANTUM ESPRESSO

Time

Section

09:00-09:15

Welcome and introduction to ENCCS

09:15-09:30

Introduction to Max-CoE and MaX flagship codes

09:30-10:00

Overview of the QE suite of codes and main features

10:00-10:25

Coffee break

10:25-13:00

PWSCF for HPC and GPU

Day 2, QUANTUM ESPRESSO

Time

Section

09:00-09:45

Introduction to Density Functional Perturbation Theory

09:45-10:15

Introduction to Time Dependent Density Functional Perturbation Theory

10:15-10:30

Coffee break

10:30-13:00

Phonons and time dependent properties on HPC and GPU

Day 3, SIESTA

Time

Section

09:00-09:45

SIESTA basics

09:45-10:30

Hands-on tutorial: A first contact with SIESTA: inputs, execution and outputs

10:30-10:45

Break

10:45-11:15

Basis sets

11:15-12:00

Hands-on tutorial: Basis set optimization

12:00-13:00

Hands-on tutorial: Convergence (k points, mesh, mixing)

Day 4, SIESTA

Time

Section

09:00-10:00

Hands-on tutorial: Moving atoms: geometry optimisation and beyond

10:30-11:00

Hands-on tutorial: Analysis tools

11:00-11:15

Break

11:15-11:45

Features available in SIESTA: spin-orbit couplings, TranSIESTA, and others

11:45-13:00

Hands-on tutorial: Pushing the boundaries of SIESTA: accelerated and massively parallel solvers

Day 5, Yambo

Time

Section

09:00-09:20

Overview of the Yambo code and its main features and performance

09:20-10:00

Introduction to the GW approximation

10:00-10:20

Coffee break

10:20-13:00

Hands-on tutorial: A guided tour through GW simulations

See also

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Credits

Contributors to this workshop:

  • Pietro Davide Delugas (SISSA)

  • Ivan Carnimeo (SISSA)

  • Oscar Baseggio (SISSA)

  • Fabrizio Ferrari Ruffino (CNR-IOM)

  • Paolo Giannozzi (CNR-IOM, UniUD)

  • Iurii Timrov (Paul Scherrer Institut)

  • Laura Bellentani (CINECA)

  • Tommaso Gorni (CINECA)

  • Aurora Ponzi (CNR-IOM)

  • Emilio Artacho (CIC NanoGUNE and University of Cambridge)

  • Catalina Coll (ICN2)

  • José Mª Escartín (ICN2)

  • Roberta Farris (ICN2)

  • Ernane de Freitas (ICN2)

  • Alberto García (ICMAB-CSIC)

  • Arnold Kole (Utrecht University)

  • Nick Papior (DTU)

  • Federico Pedron (ICN2)

  • Miguel Pruneda (CINN-CSIC)

  • José Ángel Silva Guillén (IMDEA Nanociencia)

    1. Varsano (CNR-NANO)

    1. Ferretti (CNR-NANO)

    1. Sangalli (CNR-ISM)

    1. Guandalini (Univ. of Rome, La Sapienza)

    1. Paleari (CNR-NANO)

    1. D’Alessio (Univ. Modena and Reggio Emilia, CNR-NANO)

    1. Sesti (CNR-NANO)

    1. Spallanzani (CNR-NANO)

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SIESTA

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