CECAM VIRTUAL 2021: Difference between revisions

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=== Setting up the Yambo Container===
=== Setting up the Yambo Container===


An alternative to get the Yambo code is to install the Yambo container in your machine and this can be done in few steps:
- Install [[Yambo via Docker|Yambo via Docker]] on your laptop / desktop


* Install the docker platform (Linux or Mac). Follow the instruction in the docker [https://docs.docker.com/engine/install/ website].
=== Install Yambo ===
* Pull the Yambo container:
If you have some experience with compiling codes, you can [[Download| get the source]] and [[Installation | install]] it. If you never compiled a code, it is better to choose one of the above options as the technical assistance we can offer is limited.


  sudo docker pull nicspalla/yambo-gcc_openmp_petsc:latest
== Tutorials ==


sudo it is not necessary if your user is part of the group named docker (suggested on Linux!).
Before starting, [[Get_Tutorial_files_CECAM2021|get the tutorial files]].


For Linux users:
=== Thursday 8 April ===
'''14:00 - 14:30 Hands-on setup '''


  sudo groupadd docker
'''14:30 - 17:00 From the DFT ground state to the complete setup of a Many Body calculation using Yambo''', Davide Sangalli (CNR-ISM, Italy), Pedro Melo (University of Utrecht, the Netherlands)
  sudo usermod -aG docker $USER
<!-- * [[First steps: a walk through from DFT to optical properties]] (modular) -->
<!-- * [[First steps: walk through from DFT to RPA (standalone)]] -->
* [[First steps: walk through from DFT(standalone)|First steps: Initialization and more ]]
* [[Next steps: RPA calculations (standalone)|Next steps: RPA calculations ]]


For Mac users:
=== Friday 9 April ===


  sudo dscl . create /Groups/docker
'''13:30 - 16:30 A complete tour through GW simulation in a complex material (from the blackboard to numerical computation: convergence, algorithms, parallel usage)''', Daniele Varsano (CNR-NANO, Italy), Andrea Ferretti (CNR-NANO, Italy)
  sudo dseditgroup -o edit -a $USER -t user docker


Log out and log back in so that your group membership is re-evaluated.
* [[GW hBN Yambo Virtual 2021 version|How to obtain the quasi-particle band structure of a bulk material: h-BN]]


* You are done. To run Yambo into the container:
=== Thursday 15 April ===


docker run -ti --user $(id -u):$(id -g) \
'''13:30 to 15: Calculating optical spectra including excitonic effects: a step-by-step guide'''
    --mount type=bind,source="$(pwd)",target=/tmpdir \
    -e OMP_NUM_THREADS=4  \
    nicspalla/yambo-gcc_openmp_petsc:latest \
    yambo -F yambo.in -J yambo.out


Otherwise (suggested!), copy and paste the code below in a file, i.e called drun.sh:
'''15 to 16:30: Analysis of excitonic spectra, BSE solvers and convergence''' Fulvio Paleari (CNR-ISM, Italy), Myrta Gr&#252;ning (Queen's University Belfast, Northern Ireland)


#!/bin/bash
* [[BSE hBN Yambo Virtual 2021 version|How to obtain an optical spectrum]]
docker run -ti --user $(id -u):$(id -g) \
    --mount type=bind,source="$(pwd)",target=/tmpdir \
    -e OMP_NUM_THREADS=4  \
    nicspalla/yambo-gcc_openmp_petsc:latest $@


then give the file execute privileges:
== Lectures ==


chmod +x drun.sh
All the lectures will be available in the Yambo-code YouTube [https://www.youtube.com/channel/UCO3LzAqb9W2Qk4EbG_83ATw channel]


Move (or copy) this file in the directory where you want to use Yambo and use it as prefix of your Yambo calculation:
=== Thursday 8 April ===


./drun.sh yambo -F yambo.in -J yambo.out
'''10:00 to 10:10 - Welcome & Introduction''', Daniele Varsano (CNR-NANO, Italy)


If the yambo container is working correctly you should obtain:
'''10:10 to 10:30 - [https://www.youtube.com/watch?v=Slk_wrAwekk&list=PLOvKdkt7HrnJp8nXvphzYHyPbnuBog4Dr Material Science and Yambo, what we can calculate]''',  Andrea Marini (CNR-ISM, Italy)


./drun.sh yambo
'''10:40 to 11:00 - [https://www.youtube.com/watch?v=63VJgClpQn8&list=PLOvKdkt7HrnJp8nXvphzYHyPbnuBog4Dr Introduction to Many Body Perturbation Theory]''', Pedro Melo (University of Utrecht, the Netherlands)
yambo: cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)


./drun.sh yambo -h
'''11:25 to 11:45 - [https://www.youtube.com/watch?v=jF5ABGPPsvo&list=PLOvKdkt7HrnJp8nXvphzYHyPbnuBog4Dr The linear response theory]''', Claudio Attaccalite (CNRS Marseille, France)


should provide in output the help for yambo usage.
'''12:00 to 12:20 - [https://www.youtube.com/watch?v=J6TvJuv3QqI&list=PLOvKdkt7HrnJp8nXvphzYHyPbnuBog4Dr From equations to simulations: the hard life of a Materials scientist]''', Myrta Gr&#252;ning (Queen's University Belfast, Northern Ireland)


=== Install Yambo ===  
=== Friday 9 April ===
If you have some experience with compiling codes, you can [[Download| get the source]] and [[Installation | install]] it. If you never compiled a code, it is better to choose one of the above options as the technical assistance we can offer is limited.
 
 
'''10:00 to 10:30 - [https://www.youtube.com/watch?v=odtuNbM1WRE&list=PLOvKdkt7HrnJp8nXvphzYHyPbnuBog4Dr ARPES, quasiparticles and lifetimes: A theory overview]''', Andrea Ferretti (CNR-NANO, Italy)
 
'''11:10 to 11:40 - [https://www.youtube.com/watch?v=w-UUL43tNDQ&list=PLOvKdkt7HrnJp8nXvphzYHyPbnuBog4Dr GW implementation and common approximations]''', Daniele Varsano (CNR-NANO, Italy)
 
=== Thursday 15 April ===
 
'''10:00 to 10:20 - [https://www.youtube.com/watch?v=0m6Tu8qTz2k&t=274s Optical properties & excitons]''', Maurizia Palummo (Uni Roma2 Tor Vergata, Italy)
 
'''10:30 to 10:50 - [https://www.youtube.com/watch?v=v32jr3PrfAc&t=2s Derivation of the Bethe-Salpeter Equation and main physical concepts] ''', Claudio Attaccalite (CNRS Marseille, France)
 
'''11:20 to 11:40 - [https://www.youtube.com/watch?v=UwL6GuAAsRw&t=1s BSE implementation and common approximations]''', Davide Sangalli (CNR-ISM, Italy)
 
=== Friday 16 April ===
 
'''14:00 to 14:30 - [https://www.youtube.com/watch?v=LUhPzpz__10&t=1s Electron-phonon coupling  in Yambo] ''' A.Marini
 
'''14:40 to 15:10 -  [https://www.youtube.com/watch?v=i3uVgytO4qc&t=1s Yambo parallelism and HPC] '''  A. Ferretti
 
'''15:30 to 16:10 - Parallel session in thematic rooms'''
*Room A :  [https://www.youtube.com/watch?v=gjYFpeIwyg0 Non-linear optics] C. Attaccalite and M. Gruning
*Room B : Automatisation and post processing with python layers F. Paleari and M. Bonacci
'''16:10 to 16:15 - Concluding remarks '''


== Tutorials ==
== Lecturers ==


Before starting, [[Get_Tutorial_files_CECAM2021|get the tutorial files]].


=== Thursday 8 April ===
Claudio Attaccalite (CNRS Marseille, France)
'''14:00 - 14:30 Hands-on setup '''


'''14:30 - 17:00 From the DFT ground state to the complete setup of a Many Body calculation using Yambo''' Davide Sangalli (CNR-ISM, Italy), Pedro Melo (University of Utrecht, the Netherlands)
Miki Bonacci (CNR-Nano, University of Modena, Italy)
<!-- * [[First steps: a walk through from DFT to optical properties]] (modular) -->
<!-- * [[First steps: walk through from DFT to RPA (standalone)]] -->
* [[First steps: walk through from DFT(standalone)|First steps: Initialization and more ]]
* [[Next steps: RPA calculations (standalone)|Next steps: RPA calculations ]]


=== Friday 9 April ===
Andrea Ferretti (CNR-Nano, Italy)


'''13:30 - 16:30 A complete tour through GW simulation in a complex material (from the blackboard to numerical computation: convergence, algorithms, parallel usage)''' Daniele Varsano (CNR-NANO, Italy), Andrea Ferretti (CNR-NANO, Italy)
Myrta Gr&#252;ning (Queen's University Belfast, Northern Ireland)


* [[GW hBN Yambo Virtual 2021 version|How to obtain the quasi-particle band structure of a bulk material: h-BN]]
Andrea Marini (CNR-ISM, Italy)


=== Thursday 15 April ===
Pedro Melo (University of Utrecht, the Netherlands)


'''13:30 to 15: Calculating optical spectra including excitonic effects: a step-by-step guide'''
Fulvio Paleari  (CNR-ISM, Italy)


'''15 to 16:30: Analysis of excitonic spectra, BSE solvers and convergence''' Fulvio Paleari (CNR-ISM, Italy), Myrta Gr&#252;ning (Queen's University Belfast, Northern Ireland)
Maurizia Palummo (Uni Roma2 Tor Vergata, Italy)


* [[BSE hBN Yambo Virtual 2021 version|How to obtain an optical spectrum]]
Davide Sangalli (CNR-ISM, Italy)


== Lectures ==
Daniele Varsano (CNR-Nano, Italy)


All the lectures will be available in the Yambo-code YouTube [https://www.youtube.com/channel/UCO3LzAqb9W2Qk4EbG_83ATw channel]
== Tutors ==


=== Thursday 8 April ===
Ridwan Agbaoye (Federal University of Agriculture, Abeokuta, Nigeria)


'''10:00 to 10:10 - Welcome & Introduction''' Daniele Varsano
Ignacio Alliati (Queen's University Belfast, UK)


'''10:10 to 10:30 - Material Science and Yambo, what we can calculate'''  Andrea Marini
Samaneh Ataei (Shahid Beheshti University, Iran)


'''10:40 to 11:00 - Introduction to Many Body Perturbation Theory''' Pedro Melo
Claudia Cardoso  (CNR-Nano, Italy)


'''11:25 to 11:45 - The linear response theory''' Claudio Attaccalite
Alberto Guandalini (CNR-Nano, Italy)


'''12:00 to 12:20 - From equations to simulations: the hard life of a Materials scientist''' Myrta Gr&#252;ning
Conor Hogan (CNR-ISM, Italy)


=== Friday 9 April ===
Antimo Marrazzo (EPFL, Switzerland)


Elena Molteni  (CNR-ISM, Italy)


'''10:00 to 10:20 - from ARPES to quasiparticles''' Andrea Ferretti
Daniel Murphy (Queen's University Belfast, UK)


'''10:30 to 10:50 - The Quasi Particle concept and the GW method''' Andrea Ferretti
Bo Peng (University of Cambridge, UK)


'''11:20 to 11:40 - GW implementation and common approximations''' Daniele Varsano
Michele Re Fiorentin (Politecnico di Torino, Italy)


=== Thursday 15 April ===
Dario A. Leon Valido  (CNR-Nano, University of Modena, Italy)


'''10:00 to 10:20 - Optical properties & excitons''' Maurizia Palummo
Matteo Zanfrognini  (CNR-Nano, University of Modena, Italy)


'''10:30 to 10:50 - Derivation of the Bethe-Salpeter Equation and main physical concepts''' Claudio Attaccalite
== Technical Support ==


'''11:20 to 11:40 - BSE implementation and common approximations''' Davide Sangalli
Nicola Spallanzani (CNR-NANO, Italy)

Latest revision as of 15:15, 28 March 2022

Plan for the CECAM VIRTUAL 2021 school tutorials. https://www.cecam.org/workshop-details/1081

Click to enlarge the full program

Setting up Yambo

In order to get the yambo code in your machine you have multiple options:

  • Yambo Virtual Machine
  • Yambo Container
  • Install the Yambo source in your computer

Setting up the Yambo Virtual Machine

The tutorials can be run on a dedicated Virtual Machine (called Yambo Quantum Mobile and adapted from the Quantum Mobile VM). This is run by installing it as Virtual Machine with the VirtualBox program. To install the Yambo VM in your computer you need to:

  • Download and install Virtualbox software
  • Download the Yambo Virtual Machine image
  • Install the Yambo Virtual Machine
  • Start the Yambo Virtual Machine
  • Update and install the Tutorials

To this end follow exactly the step listed here: Install the Yambo Quantum Mobile VM

Setting up the Yambo Container

- Install Yambo via Docker on your laptop / desktop

Install Yambo

If you have some experience with compiling codes, you can get the source and install it. If you never compiled a code, it is better to choose one of the above options as the technical assistance we can offer is limited.

Tutorials

Before starting, get the tutorial files.

Thursday 8 April

14:00 - 14:30 Hands-on setup

14:30 - 17:00 From the DFT ground state to the complete setup of a Many Body calculation using Yambo, Davide Sangalli (CNR-ISM, Italy), Pedro Melo (University of Utrecht, the Netherlands)

Friday 9 April

13:30 - 16:30 A complete tour through GW simulation in a complex material (from the blackboard to numerical computation: convergence, algorithms, parallel usage), Daniele Varsano (CNR-NANO, Italy), Andrea Ferretti (CNR-NANO, Italy)

Thursday 15 April

13:30 to 15: Calculating optical spectra including excitonic effects: a step-by-step guide

15 to 16:30: Analysis of excitonic spectra, BSE solvers and convergence Fulvio Paleari (CNR-ISM, Italy), Myrta Grüning (Queen's University Belfast, Northern Ireland)

Lectures

All the lectures will be available in the Yambo-code YouTube channel

Thursday 8 April

10:00 to 10:10 - Welcome & Introduction, Daniele Varsano (CNR-NANO, Italy)

10:10 to 10:30 - Material Science and Yambo, what we can calculate, Andrea Marini (CNR-ISM, Italy)

10:40 to 11:00 - Introduction to Many Body Perturbation Theory, Pedro Melo (University of Utrecht, the Netherlands)

11:25 to 11:45 - The linear response theory, Claudio Attaccalite (CNRS Marseille, France)

12:00 to 12:20 - From equations to simulations: the hard life of a Materials scientist, Myrta Grüning (Queen's University Belfast, Northern Ireland)

Friday 9 April

10:00 to 10:30 - ARPES, quasiparticles and lifetimes: A theory overview, Andrea Ferretti (CNR-NANO, Italy)

11:10 to 11:40 - GW implementation and common approximations, Daniele Varsano (CNR-NANO, Italy)

Thursday 15 April

10:00 to 10:20 - Optical properties & excitons, Maurizia Palummo (Uni Roma2 Tor Vergata, Italy)

10:30 to 10:50 - Derivation of the Bethe-Salpeter Equation and main physical concepts , Claudio Attaccalite (CNRS Marseille, France)

11:20 to 11:40 - BSE implementation and common approximations, Davide Sangalli (CNR-ISM, Italy)

Friday 16 April

14:00 to 14:30 - Electron-phonon coupling in Yambo A.Marini

14:40 to 15:10 - Yambo parallelism and HPC A. Ferretti

15:30 to 16:10 - Parallel session in thematic rooms

  • Room A : Non-linear optics C. Attaccalite and M. Gruning
  • Room B : Automatisation and post processing with python layers F. Paleari and M. Bonacci

16:10 to 16:15 - Concluding remarks

Lecturers

Claudio Attaccalite (CNRS Marseille, France)

Miki Bonacci (CNR-Nano, University of Modena, Italy)

Andrea Ferretti (CNR-Nano, Italy)

Myrta Grüning (Queen's University Belfast, Northern Ireland)

Andrea Marini (CNR-ISM, Italy)

Pedro Melo (University of Utrecht, the Netherlands)

Fulvio Paleari (CNR-ISM, Italy)

Maurizia Palummo (Uni Roma2 Tor Vergata, Italy)

Davide Sangalli (CNR-ISM, Italy)

Daniele Varsano (CNR-Nano, Italy)

Tutors

Ridwan Agbaoye (Federal University of Agriculture, Abeokuta, Nigeria)

Ignacio Alliati (Queen's University Belfast, UK)

Samaneh Ataei (Shahid Beheshti University, Iran)

Claudia Cardoso (CNR-Nano, Italy)

Alberto Guandalini (CNR-Nano, Italy)

Conor Hogan (CNR-ISM, Italy)

Antimo Marrazzo (EPFL, Switzerland)

Elena Molteni (CNR-ISM, Italy)

Daniel Murphy (Queen's University Belfast, UK)

Bo Peng (University of Cambridge, UK)

Michele Re Fiorentin (Politecnico di Torino, Italy)

Dario A. Leon Valido (CNR-Nano, University of Modena, Italy)

Matteo Zanfrognini (CNR-Nano, University of Modena, Italy)

Technical Support

Nicola Spallanzani (CNR-NANO, Italy)

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