Info about the hands-on courses

For the hands-on courses, participants were expected to bring their own laptops. Prior to the summer school, all participants installed an all-inclusive software container (virtual machine) on their laptop. The software and installation instructions are available here.

QE-2019 Program

Book of abstracts: (PDF, 3.8M)
Hands-on execrises: avaiable on GitLab.

Color code: Lecture (lecture-hall) Hands-on (classroom)

DAY 0: Sunday, September 15 (Basic introductory lectures)

13:30 − 14:00 Registration

14:00 − 14:45 Anton Kokalj
A chemist view of bonding & a very informal intro to Bloch theorem: from molecules to solids and back. (PDF, 9.4M)

14:45 − 15:00 Coffee break

15:00 − 18:00 Stefano Baroni
Modelling materials using quantum mechanics and digital computers: the plane-wave pseudo potenial way. (PDF, 19M)

18:00 − 19:00 Small welcome party: snacks & beverages

DAY 1: Monday, September 16

8:00 − 8:50 Registration & participant's computer setup check

8:50 − 9:00 Opening remarks. (PDF, 2.1M) General instructions. (PDF, 4.5M)

9:00 − 10:30 Paolo Giannozzi and Pietro Delugas
Quantum ESPRESSO: overview and basic functionalities. The self-consistent cycle. PBC: supercells and k-point sampling. (PDF, 1.2M)

10:30 − 11:00 Coffee break

11:00 − 12:30 Paolo Giannozzi and Pietro Delugas (contd).
Charge densities and potentials. Systems in 0-1-2-3D. Metals vs. insulators. Non-magnetic vs. magnetic systems. (PDF, 874K)

12:30 − 14:00 Lunch

14:00 − 14:30 Participant’s computer setup check (contd).

14:30 − 18:00 Hands-on. Anton Kokalj, Pietro Delugas, Andrea Urru, Matic Poberžnik, Andrijana Solajić, Jelena Pešić
Installation. SCF + basic post-processing. XCrySDen, PWgui, QE-emacs-modes, PWTK (basics). Exercises. (PDF, 3.8M)

18:00 − 18:30 Coffee break

18:30 − 19:30 Special guest lecture − Željko Šljivančanin

A short introduction to physics and chemistry at crystalline surfaces
A short introduction to physics and chemistry at crystalline surfaces
Željko ŠLJIVANČANIN
(Institute of Nuclear Sciences, Vinča, Serbia)

After a brief account of the most common ideal crystalline surfaces and their basic properties, I will describe the interaction of surfaces with atomic and molecular adsorbates. This will include modeling of simple chemical reactions at metal surfaces and the role played by structural defects. Then I will focus on graphene and efforts to modify its electronic properties via controlled hydrogenation.

Results from DFT calculations will be compared with those from the experiments, obtained using techniques such as scanning tunneling microscopy and temperature programmed desorption.

(PDF, 3.4M)

DAY 2: Tuesday, September 17

9:00 − 10:30 Paolo Giannozzi and Anton Kokalj
Forces, stresses, geometry optimisation. (PDF, 459K)
Chasing saddle points: the NEB method. (PDF, 18M)

10:30 − 11:00 Coffee break

11:00 − 12:30 Paolo Giannozzi
Advanced functionals: higher accuracy (hybrids), strongly correlated materials (DFT+U), weakly bound systems (van der Waals)
(PDF, 879K)

12:30 − 14:00 Lunch

14:00 − 18:00 Hands-on. Anton Kokalj, Iurii Timrov, Yusuf Shaidu, Matic Poberžnik, Matej Huš, Srdjan Stavrić
Optimizations, NEB, functionals. Automating the workflow with PWTK.
Part-1: (PDF, 3.1M), Part-2 (functionals): (PDF, 1.3M)

18:00 − 18:30 Coffee break

18:30 − 19:30 Special guest lecture − Iurii Timrov

First-principles quantum simulations of correlated materials using Hubbard-corrected density-functional (perturbation) theory
First-principles quantum simulations of correlated materials using Hubbard-corrected density-functional (perturbation) theory
Iurii TIMROV
(École Polytechnique Fédérale de Lausanne, Switzerland)

DFT+U and DFT+U+V are simple and powerful tools to model correlated systems containing partially-filled manifolds of localized d and f states [1]. However, the Hubbard U (on-site) and V (inter-site) parameters are often treated semi-empirically, which is a somewhat unsatisfactory approach. Conceptual and practical methods to determine e.g. the Hubbard U parameter from first principles have nevertheless been introduced long ago, based either on the constrained random-phase approximation or on linear-response theory [2]. Nonetheless, these approaches are often overlooked due to their cost and/or complexity. Here, we introduce a computationally inexpensive and straightforward approach to determine on-site U and inter-site V [3], hitherto obtained from the difference between bare and self-consistent inverse electronic susceptibilities evaluated from supercell calculations. By recasting these calculations in the language of density-functional perturbation theory (DFPT) [4] we remove the need of supercells, and allow for a fully automated determination of Hubbard parameters. Such developments open the way for deployment in high-throughput studies, while providing the community with a simple tool to calculate consistent values of U and V for any system at hand. The approach has been implemented in the Quantum ESPRESSO package [5] and is showcased with applications to selected transition-metal compounds. Lastly, we will discuss the effect of Hubbard corrections on the calculation of formation energies of systems with defects [6], phonons [7], and near-edge X-ray absorption fine structure [8].

References:
[1] V.I. Anisimov, J. Zaanen, O.K. Andersen, Phys. Rev. B 44, 943 (1991).
[2] M. Cococcioni and S. de Gironcoli, Phys. Rev. B 71, 035105 (2005).
[3] I. Timrov, N. Marzari and M. Cococcioni, Phys. Rev. B 98, 085127 (2018).
[4] S. Baroni, S. de Gironcoli, A. Dal Corso, P. Giannozzi, Rev. Mod. Phys. 73, 515 (2001).
[5] P. Giannozzi et al., J. Phys.: Condens. Matter 29, 465901 (2017).
[6] C. Ricca, I. Timrov, M. Cococcioni, N. Marzari, U. Aschauer, Phys. Rev. B 99, 094102 (2019).
[7] A. Floris, I. Timrov, B. Himmetoglu, S. de Gironcoli, N. Marzari, M. Cococcioni, in preparation.
[8] I. Timrov, P. Agrawal, S. Erat, A. Braun, M. Cococcioni, M. Calandra, N. Marzari, D. Passerone, in preparation.

(PDF, 20M)

DAY 3: Wednesday, September 18

9:00 − 10:30 Stefano Baroni
Density-functional perturbation theory: phonons (PDF, 8.1M)

10:30 − 11:00 Coffee break

11:00 − 12:30 Iurii Timrov
Time-dependent density-functional (perturbation) theory: optical absorption and electron energy loss spectroscopies (PDF, 15M)

12:30 − 14:00 Lunch

14:00 − 18:00 Hands-on. Iurii Timrov, Oscar Baseggio, Andrea Urru, Milan Jocić
(TD) DFPT
Part-1 (DFPT): (PDF, 1.8M), Part-2 (TDDFPT): (PDF, 1.3M)

18:00 − 18:30 Coffee break

18:30 − 21:00 Elevator pitches (PDF, 29M) + poster session (part I)

DAY 4:Thursday, September 19

9:00 − 10:30 Giovanni Pizzi
High-throughput computing with the AiiDA platform (PDF, 6.4M)

10:30 − 11:00 Coffee break

11:00 − 12:30 Hands-on. Giovanni Pizzi, Nicola Spallanzani, Pietro Bonfà
Hands-on AiiDA

12:30 − 14:00 Lunch

14:00 − 16:30 Hands-on. Giovanni Pizzi, Nicola Spallanzani, Pietro Bonfà
Hands-on AiiDA

16:30 − 17:00 Coffee break

17:00 − 18:00 Special guest lecture − Dino Novko

Equilibrium and ultrafast vibrational dynamics from first principles
Equilibrium and ultrafast vibrational dynamics from first principles
Dino NOVKO
(Institute of Physics, Zagreb, Croatia)

Raman spectroscopy is a powerful and widely used technique for structural characterization and quality assessment of quasi-two-dimensional and layered materials. This tool under ultrafast transient conditions can as well be utilized to investigate the photo-induced phonon or nuclear dynamics. Here I present a theoretical framework based in first principles that is able to simulate both equilibrium and non-equilibrium dynamics of phonons in metallic systems. The main relaxation mechanism in this approach is coupling between thermalized/hot electrons and system phonons (i.e., nonadiabatic electron-phonon coupling). Using this general theory I explain the anomalous Raman spectrum of MgB2 and further reveal a laser-excited non-equilibrium dynamics of E2g phonon mode in this superconductor [1,2]. As another exciting example, I simulate Raman spectra of several single-layer transition metal dichalcogenides doped with field-effect technique [3] and show how the adiabatic Born-Oppenheimer approximation breaks down unexpectedly in these cases as well.

References:
[1] D. Novko, Phys. Rev. B 98, 041112(R) (2018)
[2] D. Novko, F. Caruso, C. Draxl, E. Cappelluti, arXiv:1904.03062, (2019)
[3] B. Chakraborty et al.,Phys. Rev. B 85, 161403(R) (2012)

(PDF, 5.4M)

18:00 − 18:30 Coffee break

18:30 − 21:00 Elevator pitches (PDF, 29M) + poster session (part II)

DAY 5: Friday, September 20

9:00 − 10:30 Carlo Cavazzoni and Pietro Bonfà
Quantum ESPRESSO on HPC and GPU systems: parallelisation and hybrid architecture (PPTX, 14M)

10:30 − 11:00 Coffee break

11:00 − 12:30 Hands-on. Pietro Bonfà, Carlo Cavazzoni, Pietro Delugas, Drejc Kopač, Milan Jocić
Hands-on QE on HPC and GPU systems (PDF, 8.8M)

12:30 − 14:00 Lunch

14:00 − 16:30 Hands-on. Pietro Bonfà, Carlo Cavazzoni, Pietro Delugas, Drejc Kopač, Milan Jocić
Hands-on QE on HPC and GPU systems

16:30 − 16:45 Break

16:45 − 17:00 Poster prize award & Closing remarks (PDF, 959K)
[movie of O₂ experiment: low (AVI, 95M); high (MP4, 352M)]

13:30 − 14:00	Registration
14:00 − 14:45	Anton Kokalj A chemist view of bonding & a very informal intro to Bloch theorem: from molecules to solids and back. (PDF, 9.4M)
14:45 − 15:00	Coffee break
15:00 − 18:00	Stefano Baroni Modelling materials using quantum mechanics and digital computers: the plane-wave pseudo potenial way. (PDF, 19M)
18:00 − 19:00	Small welcome party: snacks & beverages

8:00 − 8:50	Registration & participant's computer setup check
8:50 − 9:00	Opening remarks. (PDF, 2.1M) General instructions. (PDF, 4.5M)
9:00 − 10:30	Paolo Giannozzi and Pietro Delugas Quantum ESPRESSO: overview and basic functionalities. The self-consistent cycle. PBC: supercells and k-point sampling. (PDF, 1.2M)
10:30 − 11:00	Coffee break
11:00 − 12:30	Paolo Giannozzi and Pietro Delugas (contd). Charge densities and potentials. Systems in 0-1-2-3D. Metals vs. insulators. Non-magnetic vs. magnetic systems. (PDF, 874K)
12:30 − 14:00	Lunch
14:00 − 14:30	Participant’s computer setup check (contd).
14:30 − 18:00	Hands-on. Anton Kokalj, Pietro Delugas, Andrea Urru, Matic Poberžnik, Andrijana Solajić, Jelena Pešić Installation. SCF + basic post-processing. XCrySDen, PWgui, QE-emacs-modes, PWTK (basics). Exercises. (PDF, 3.8M)
18:00 − 18:30	Coffee break
18:30 − 19:30	Special guest lecture − Željko Šljivančanin A short introduction to physics and chemistry at crystalline surfaces A short introduction to physics and chemistry at crystalline surfaces Željko ŠLJIVANČANIN (Institute of Nuclear Sciences, Vinča, Serbia) After a brief account of the most common ideal crystalline surfaces and their basic properties, I will describe the interaction of surfaces with atomic and molecular adsorbates. This will include modeling of simple chemical reactions at metal surfaces and the role played by structural defects. Then I will focus on graphene and efforts to modify its electronic properties via controlled hydrogenation. Results from DFT calculations will be compared with those from the experiments, obtained using techniques such as scanning tunneling microscopy and temperature programmed desorption. (PDF, 3.4M)

9:00 − 10:30	Paolo Giannozzi and Anton Kokalj Forces, stresses, geometry optimisation. (PDF, 459K) Chasing saddle points: the NEB method. (PDF, 18M)
10:30 − 11:00	Coffee break
11:00 − 12:30	Paolo Giannozzi Advanced functionals: higher accuracy (hybrids), strongly correlated materials (DFT+U), weakly bound systems (van der Waals) (PDF, 879K)
12:30 − 14:00	Lunch
14:00 − 18:00	Hands-on. Anton Kokalj, Iurii Timrov, Yusuf Shaidu, Matic Poberžnik, Matej Huš, Srdjan Stavrić Optimizations, NEB, functionals. Automating the workflow with PWTK. Part-1: (PDF, 3.1M), Part-2 (functionals): (PDF, 1.3M)
18:00 − 18:30	Coffee break
18:30 − 19:30	Special guest lecture − Iurii Timrov First-principles quantum simulations of correlated materials using Hubbard-corrected density-functional (perturbation) theory First-principles quantum simulations of correlated materials using Hubbard-corrected density-functional (perturbation) theory Iurii TIMROV (École Polytechnique Fédérale de Lausanne, Switzerland) DFT+U and DFT+U+V are simple and powerful tools to model correlated systems containing partially-filled manifolds of localized d and f states [1]. However, the Hubbard U (on-site) and V (inter-site) parameters are often treated semi-empirically, which is a somewhat unsatisfactory approach. Conceptual and practical methods to determine e.g. the Hubbard U parameter from first principles have nevertheless been introduced long ago, based either on the constrained random-phase approximation or on linear-response theory [2]. Nonetheless, these approaches are often overlooked due to their cost and/or complexity. Here, we introduce a computationally inexpensive and straightforward approach to determine on-site U and inter-site V [3], hitherto obtained from the difference between bare and self-consistent inverse electronic susceptibilities evaluated from supercell calculations. By recasting these calculations in the language of density-functional perturbation theory (DFPT) [4] we remove the need of supercells, and allow for a fully automated determination of Hubbard parameters. Such developments open the way for deployment in high-throughput studies, while providing the community with a simple tool to calculate consistent values of U and V for any system at hand. The approach has been implemented in the Quantum ESPRESSO package [5] and is showcased with applications to selected transition-metal compounds. Lastly, we will discuss the effect of Hubbard corrections on the calculation of formation energies of systems with defects [6], phonons [7], and near-edge X-ray absorption fine structure [8]. References: [1] V.I. Anisimov, J. Zaanen, O.K. Andersen, Phys. Rev. B 44, 943 (1991). [2] M. Cococcioni and S. de Gironcoli, Phys. Rev. B 71, 035105 (2005). [3] I. Timrov, N. Marzari and M. Cococcioni, Phys. Rev. B 98, 085127 (2018). [4] S. Baroni, S. de Gironcoli, A. Dal Corso, P. Giannozzi, Rev. Mod. Phys. 73, 515 (2001). [5] P. Giannozzi et al., J. Phys.: Condens. Matter 29, 465901 (2017). [6] C. Ricca, I. Timrov, M. Cococcioni, N. Marzari, U. Aschauer, Phys. Rev. B 99, 094102 (2019). [7] A. Floris, I. Timrov, B. Himmetoglu, S. de Gironcoli, N. Marzari, M. Cococcioni, in preparation. [8] I. Timrov, P. Agrawal, S. Erat, A. Braun, M. Cococcioni, M. Calandra, N. Marzari, D. Passerone, in preparation. (PDF, 20M)

9:00 − 10:30	Stefano Baroni Density-functional perturbation theory: phonons (PDF, 8.1M)
10:30 − 11:00	Coffee break
11:00 − 12:30	Iurii Timrov Time-dependent density-functional (perturbation) theory: optical absorption and electron energy loss spectroscopies (PDF, 15M)
12:30 − 14:00	Lunch
14:00 − 18:00	Hands-on. Iurii Timrov, Oscar Baseggio, Andrea Urru, Milan Jocić (TD) DFPT Part-1 (DFPT): (PDF, 1.8M), Part-2 (TDDFPT): (PDF, 1.3M)
18:00 − 18:30	Coffee break
18:30 − 21:00	Elevator pitches (PDF, 29M) + poster session (part I)

9:00 − 10:30	Giovanni Pizzi High-throughput computing with the AiiDA platform (PDF, 6.4M)
10:30 − 11:00	Coffee break
11:00 − 12:30	Hands-on. Giovanni Pizzi, Nicola Spallanzani, Pietro Bonfà Hands-on AiiDA
12:30 − 14:00	Lunch
14:00 − 16:30	Hands-on. Giovanni Pizzi, Nicola Spallanzani, Pietro Bonfà Hands-on AiiDA
16:30 − 17:00	Coffee break
17:00 − 18:00	Special guest lecture − Dino Novko Equilibrium and ultrafast vibrational dynamics from first principles Equilibrium and ultrafast vibrational dynamics from first principles Dino NOVKO (Institute of Physics, Zagreb, Croatia) Raman spectroscopy is a powerful and widely used technique for structural characterization and quality assessment of quasi-two-dimensional and layered materials. This tool under ultrafast transient conditions can as well be utilized to investigate the photo-induced phonon or nuclear dynamics. Here I present a theoretical framework based in first principles that is able to simulate both equilibrium and non-equilibrium dynamics of phonons in metallic systems. The main relaxation mechanism in this approach is coupling between thermalized/hot electrons and system phonons (i.e., nonadiabatic electron-phonon coupling). Using this general theory I explain the anomalous Raman spectrum of MgB2 and further reveal a laser-excited non-equilibrium dynamics of E2g phonon mode in this superconductor [1,2]. As another exciting example, I simulate Raman spectra of several single-layer transition metal dichalcogenides doped with field-effect technique [3] and show how the adiabatic Born-Oppenheimer approximation breaks down unexpectedly in these cases as well. References: [1] D. Novko, Phys. Rev. B 98, 041112(R) (2018) [2] D. Novko, F. Caruso, C. Draxl, E. Cappelluti, arXiv:1904.03062, (2019) [3] B. Chakraborty et al.,Phys. Rev. B 85, 161403(R) (2012) (PDF, 5.4M)
18:00 − 18:30	Coffee break
18:30 − 21:00	Elevator pitches (PDF, 29M) + poster session (part II)

9:00 − 10:30	Carlo Cavazzoni and Pietro Bonfà Quantum ESPRESSO on HPC and GPU systems: parallelisation and hybrid architecture (PPTX, 14M)
10:30 − 11:00	Coffee break
11:00 − 12:30	Hands-on. Pietro Bonfà, Carlo Cavazzoni, Pietro Delugas, Drejc Kopač, Milan Jocić Hands-on QE on HPC and GPU systems (PDF, 8.8M)
12:30 − 14:00	Lunch
14:00 − 16:30	Hands-on. Pietro Bonfà, Carlo Cavazzoni, Pietro Delugas, Drejc Kopač, Milan Jocić Hands-on QE on HPC and GPU systems
16:30 − 16:45	Break
16:45 − 17:00	Poster prize award & Closing remarks (PDF, 959K) [movie of O₂ experiment: low (AVI, 95M); high (MP4, 352M)]