Difference between revisions of "Tutorials"

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== Tutorial files ==
== Tutorial files ==


The tutorial CORE databases can be downloaded one by one via the link provided below or by using the yambo GIT tutorial repository (advanced users only).
The tutorial CORE databases can be obtained


=== Tutorial Repository (advanced users) ===
* from the [[Yambo_Virtual_Machine|Yambo Virtual Machine]]
The [https://github.com/yambo-code/tutorials tutorials repository] contains the most updated tutorials CORE databases. To use it
* from the Yambo web-page
$ git clone https://github.com/yambo-code/tutorials.git YAMBO_TUTORIALS
* from the Yambo GIT tutorial repository
$ cd YAMBO_TUTORIALS
 
$ ./setup.pl -install
=== From the Yambo Virtual Machine (VM) ===
If you are using the VM, a recent version of the tutorial files is provided.Follow these [[Yambo_Virtual_Machine#Updating_the_Yambo_tutorial_files| instructions]] to update the tutorial files to the most recent version.
 
=== From the Yambo website ===
If you are using your own installation or the docker, the files needed to run the tutorials can be downloaded from the lists below.  


=== Direct Download (all users) ===
After downloading the tar.gz files just unpack them in '''the YAMBO_TUTORIALS''' folder. For example
The tutorials can be also downloaded together with the DFT input files. After downloading the tar.gz files just unpack them in '''the YAMBO_TUTORIALS''' folder. For example
  $ mkdir YAMBO_TUTORIALS
  $ mkdir YAMBO_TUTORIALS
  $ mv hBN.tar.gz YAMBO_TUTORIALS
  $ mv hBN.tar.gz YAMBO_TUTORIALS
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====Files needed for modular tutorials====
====Files needed for modular tutorials====
All of the following should be downloaded prior to following the modular tutorials:<br>
All of the following should be downloaded prior to following the modular tutorials:<br>
[http://www.yambo-code.org/educational/tutorials/files/hBN.tar.gz hBN.tar.gz]
[https://www.yambo-code.org/educational/tutorials/files/hBN.tar.gz hBN.tar.gz],
[http://www.yambo-code.org/educational/tutorials/files/hBN-2D.tar.gz hBN-2D.tar.gz]
[https://www.yambo-code.org/educational/tutorials/files/hBN-convergence-kpoints.tar.gz hBN-convergence-kpoints.tar.gz],
[http://www.yambo-code.org/educational/tutorials/files/hBN-2D-para.tar.gz hBN-2D-para.tar.gz]
[https://www.yambo-code.org/educational/tutorials/files/hBN-2D.tar.gz hBN-2D.tar.gz],
[https://www.yambo-code.org/educational/tutorials/files/hBN-2D-para.tar.gz hBN-2D-para.tar.gz],
<br>
[https://www.yambo-code.org/educational/tutorials/files/hBN_DBs.tar.gz hBN_DBs.tar.gz],
[https://www.yambo-code.org/educational/tutorials/files/hBN-convergence-kpoints_DBs.tar.gz hBN-convergence-kpoints_DBs.tar.gz],
[https://www.yambo-code.org/educational/tutorials/files/hBN-2D_DBs.tar.gz hBN-2D_DBs.tar.gz],
[https://www.yambo-code.org/educational/tutorials/files/hBN-2D-para_DBs.tar.gz hBN-2D-para_DBs.tar.gz]


====Files needed for stand-alone tutorials====
====Files needed for stand-alone tutorials====
At the start of each tutorial you will be told which specific file needs to be downloaded:<br>
At the start of each tutorial you will be told which specific file needs to be downloaded:<br>
[http://www.yambo-code.org/educational/tutorials/files/Silicon.tar.gz Silicon.tar.gz]
[https://www.yambo-code.org/educational/tutorials/files/Silicon.tar.gz Silicon.tar.gz],
[http://www.yambo-code.org/educational/tutorials/files/LiF.tar.gz LiF.tar.gz]
[https://www.yambo-code.org/educational/tutorials/files/LiF.tar.gz LiF.tar.gz]
<br>
[https://www.yambo-code.org/educational/tutorials/files/Silicon_DBs.tar.gz Silicon_DBs.tar.gz],
[https://www.yambo-code.org/educational/tutorials/files/LiF_DBs.tar.gz LiF_DBs.tar.gz],
<!--
<!--
[http://www.yambo-code.org/educational/tutorials/files/Si_surface.tar.gz Si_surface.tar.gz]
[https://www.yambo-code.org/educational/tutorials/files/Si_surface.tar.gz Si_surface.tar.gz]
[http://www.yambo-code.org/educational/tutorials/files/Si_wire.tar.gz Si_wire.tar.gz]
[https://www.yambo-code.org/educational/tutorials/files/Si_wire.tar.gz Si_wire.tar.gz]
[http://www.yambo-code.org/educational/tutorials/files/H2.tar.gz H2.tar.gz]
[https://www.yambo-code.org/educational/tutorials/files/H2.tar.gz H2.tar.gz]
-->
-->
[http://www.yambo-code.org/educational/tutorials/files/Aluminum.tar.gz Aluminum.tar.gz]
[https://www.yambo-code.org/educational/tutorials/files/Aluminum.tar.gz Aluminum.tar.gz],
<!--[http://www.yambo-code.org/educational/tutorials/files/GaSb.tar.gz GaSb.tar.gz]-->
<!--[https://www.yambo-code.org/educational/tutorials/files/GaSb.tar.gz GaSb.tar.gz]-->
[http://www.yambo-code.org/educational/tutorials/files/Hydrogen_Chain.tar.gz Hydrogen_Chain.tar.gz]
[https://www.yambo-code.org/educational/tutorials/files/Hydrogen_Chain.tar.gz Hydrogen_Chain.tar.gz]
<br>
[https://www.yambo-code.org/educational/tutorials/files/Aluminum_DBs.tar.gz Aluminum_DBs.tar.gz],
[https://www.yambo-code.org/educational/tutorials/files/Hydrogen_Chain_DBs.tar.gz Hydrogen_Chain_DBs.tar.gz]
<br>
[https://www.yambo-code.org/educational/tutorials/files/si.epc.tgz si.epc.tgz]
[https://www.yambo-code.org/educational/tutorials/files/si_freqs_files.tgz si_freqs_files.tgz]
 
=== From the Git Tutorial Repository (advanced users) ===
If you are using your own installation or the docker, the [https://github.com/yambo-code/tutorials tutorials repository] contains the updated tutorials CORE databases. To use it
$ git clone https://github.com/yambo-code/tutorials.git YAMBO_TUTORIALS
$ cd YAMBO_TUTORIALS
$ ./setup.pl -install


== <span id="Stand-alone overview"></span>Stand-alone tutorials ==
== <span id="Stand-alone overview"></span>Stand-alone tutorials ==
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These tutorials can be accessed directly from this page of from the side bar. They include different kind of subjects:
These tutorials can be accessed directly from this page of from the side bar. They include different kind of subjects:
'''Warning''': These tutorials were prepared using previous version of the Yambo code: some command lines, variables, reports and outputs can be  slightly different from the last version of the code.  Scripts for parsing output cannot work anymore and should be edited to work with the new outputs. New command lines can be accessed typing <code>yambo -h </code>


=== Basic ===
=== Basic ===
* [[LiF|Linear Response in 3D. Excitons at work]]
* [[LiF|Linear Response in 3D. Excitons at work]]
* [[Silicon|GW convergence]]
<!--
<!--
* [[Si_Surface|Linear Response in 2D]]
* [[Si_Surface|Linear Response in 2D]]
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* [[H2|Linear Response in 0D]]
* [[H2|Linear Response in 0D]]
-->
-->
* [[Silicon|GW convergence]]
=== Post Processing ===
* [[Yambo Post Processing (ypp)]]
* [https://www.yambo-code.org/wiki/index.php?title=First_steps_in_Yambopy First Steps in YamboPy]
* [https://www.yambo-code.org/wiki/index.php?title=Yambopy_tutorial:_band_structures Yambopy tutorial: band structures]
* [https://www.yambo-code.org/wiki/index.php?title=Yambopy_tutorial:_Yambo_databases Yambopy tutorial: Yambo databases]


=== Advanced ===
=== Advanced ===
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* [[Electron Phonon Coupling|Electron Phonon Coupling]]
* [[Electron Phonon Coupling|Electron Phonon Coupling]]
* [[Optical properties at finite temperature]]
* [[Optical properties at finite temperature]]
* [[Phonon-assisted luminescence by finite atomic displacements]]
* [[Exciton-phonon coupling and luminescence]]


==== Non linear response ====
==== Non linear response ====
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* [http://www.attaccalite.com/lumen/thg_in_silicon.html Third Harmonic Generation]
* [http://www.attaccalite.com/lumen/thg_in_silicon.html Third Harmonic Generation]
* [http://www.attaccalite.com/lumen/spin_orbit.html Spin-orbit coupling and non-linear response]
* [http://www.attaccalite.com/lumen/spin_orbit.html Spin-orbit coupling and non-linear response]
* [http://www.attaccalite.com/lumen/dealing_with_large_systems.html Parallelization for nonlinear response (old tutorial)]
* [[Two-photon absorption]]
* [[Pump and Probe]]
* [[Parallelization for non-linear response calculations]]
 
==== Developing Yambo ====
 
* [[How to create a new project in Yambo]]
* [[How to create a new ypp interface]]
* [[Some hints on github]]
<!--
<!--


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== <span id="Modular overview"></span>Modular tutorials ==
== <span id="Modular overview"></span>Modular tutorials ==
These tutorials are designed to provide a deeper understanding of specific yambo tasks and runlevels. They are designed to avoid repetition of common procedures and physical concepts. As such, they make use of the same physical systems: bulk hexagonal boron nitride ''hBN'' and a hBN sheet ''hBN-2D''.
These tutorials are designed to provide a deeper understanding of specific yambo tasks and runlevels. They are designed to avoid repetition of common procedures and physical concepts. As such, they make use of the same physical systems: bulk hexagonal boron nitride ''hBN'' and a hBN sheet ''hBN-2D''.
Files for both systems must be downloaded, and make sure to extract the tarballs '''in the same place.'''


'''Download:'''
'''Warning''': These tutorials were prepared using previous version of the Yambo code: some command lines, variables, reports and outputs can be  slightly different from the last version of the code. Scripts for parsing output cannot work anymore and should be edited to work with the new outputs. New command lines can be accessed typing <code>yambo -h </code>
[http://www.yambo-code.org/educational/tutorials/files/hBN.tar.gz hBN.tar.gz]
[http://www.yambo-code.org/educational/tutorials/files/hBN-2D.tar.gz hBN-2D.tar.gz]
[http://www.yambo-code.org/educational/tutorials/files/hBN-2D-para.tar.gz hBN-2D-para.tar.gz]


====Introduction====
====Introduction====
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<!--* [[Two particle excitations]] (try to bypass this page) : Learn how to set up and run calculations to obtain and analyze an optical absorption spectrum of bulk and low dimension materials by using the Bethe-Salpeter equation-->
<!--* [[Two particle excitations]] (try to bypass this page) : Learn how to set up and run calculations to obtain and analyze an optical absorption spectrum of bulk and low dimension materials by using the Bethe-Salpeter equation-->


====Yambo-python driver====
====Yambopy====
* [[First steps in Yambopy]]
* [[First steps in Yambopy]]
* [[GW tutorial. Convergence and approximations (BN)]]
* [[GW tutorial. Convergence and approximations (BN)]]
* [[Bethe-Salpeter equation tutorial. Optical absorption (BN)]]
* [[Bethe-Salpeter equation tutorial. Optical absorption (BN)]]
* [[Yambopy tutorial: band structures | Database and plotting tutorial for quantum espresso: qepy]]
* [[Yambopy tutorial: Yambo databases | Database and plotting tutorial for yambo: yambopy ]]


<!--
<!--
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=== Modules ===
=== Modules ===
Alternatively, users can learn more about a specific runlevel or task by looking at the individual '''[[Modules|documentation modules]]'''. These provide a focus on the input parameters, run time behaviour, and underlying physics. Although they can be followed separately, non-experts are urged to follow them as part of the more structured tutorials given above.
Alternatively, users can learn more about a specific runlevel or task by looking at the individual '''[[Modules|documentation modules]]'''. These provide a focus on the input parameters, run time behaviour, and underlying physics. Although they can be followed separately, non-experts are urged to follow them as part of the more structured tutorials given above.


== <span id="Schools"></span>Schools ==
== <span id="Schools"></span>Schools ==
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* [[ICTP2020]]
* [[ICTP2020]]
* [[CECAM VIRTUAL 2021]]
* [[CECAM VIRTUAL 2021]]
* [https://www.yambo-code.org/wiki/index.php?title=ICTP_2022 ICTP2022]

Revision as of 11:43, 19 April 2022


If you are starting out with Yambo, or even an experienced user, we recommend that you complete the following tutorials before trying to use Yambo for your system.

The tutorials are meant to give some introductory background to the key concepts behind Yambo. Practical topics such as convergence are also discussed. Nonetheless, users are invited to first read and study the background material in order to get familiar with the fundamental physical quantities.

Two kinds of tutorials are provided: stand-alone and modular.

Tutorial files

The tutorial CORE databases can be obtained

From the Yambo Virtual Machine (VM)

If you are using the VM, a recent version of the tutorial files is provided.Follow these instructions to update the tutorial files to the most recent version.

From the Yambo website

If you are using your own installation or the docker, the files needed to run the tutorials can be downloaded from the lists below.

After downloading the tar.gz files just unpack them in the YAMBO_TUTORIALS folder. For example

$ mkdir YAMBO_TUTORIALS
$ mv hBN.tar.gz YAMBO_TUTORIALS
$ cd YAMBO_TUTORIALS
$ tar -xvfz hBN.tar.gz
$ ls YAMBO_TUTORIALS
  hBN

Files needed for modular tutorials

All of the following should be downloaded prior to following the modular tutorials:
hBN.tar.gz, hBN-convergence-kpoints.tar.gz, hBN-2D.tar.gz, hBN-2D-para.tar.gz,
hBN_DBs.tar.gz, hBN-convergence-kpoints_DBs.tar.gz, hBN-2D_DBs.tar.gz, hBN-2D-para_DBs.tar.gz

Files needed for stand-alone tutorials

At the start of each tutorial you will be told which specific file needs to be downloaded:
Silicon.tar.gz, LiF.tar.gz
Silicon_DBs.tar.gz, LiF_DBs.tar.gz, Aluminum.tar.gz, Hydrogen_Chain.tar.gz
Aluminum_DBs.tar.gz, Hydrogen_Chain_DBs.tar.gz
si.epc.tgz si_freqs_files.tgz

From the Git Tutorial Repository (advanced users)

If you are using your own installation or the docker, the tutorials repository contains the updated tutorials CORE databases. To use it

$ git clone https://github.com/yambo-code/tutorials.git YAMBO_TUTORIALS
$ cd YAMBO_TUTORIALS
$ ./setup.pl -install

Stand-alone tutorials

These tutorials are self-contained and cover a variety of mixed topics, both physical and methodological. They are designed to be followed from start to finish in one page and do not require previous knowledge of yambo. Each tutorial requires download of a specific core database, and typically they cover a specific physical system (like bulk GaSb or a hydrogen chain). Ground state input files and pseudopotentials are provided. Output files are also provided for reference.

These tutorials can be accessed directly from this page of from the side bar. They include different kind of subjects:

Warning: These tutorials were prepared using previous version of the Yambo code: some command lines, variables, reports and outputs can be slightly different from the last version of the code. Scripts for parsing output cannot work anymore and should be edited to work with the new outputs. New command lines can be accessed typing yambo -h


Basic

Post Processing

Advanced

GW and Quasi-particles

Electron phonon coupling

Non linear response

Developing Yambo


Modular tutorials

These tutorials are designed to provide a deeper understanding of specific yambo tasks and runlevels. They are designed to avoid repetition of common procedures and physical concepts. As such, they make use of the same physical systems: bulk hexagonal boron nitride hBN and a hBN sheet hBN-2D.

Warning: These tutorials were prepared using previous version of the Yambo code: some command lines, variables, reports and outputs can be slightly different from the last version of the code. Scripts for parsing output cannot work anymore and should be edited to work with the new outputs. New command lines can be accessed typing yambo -h

Introduction

Quasiparticles in the GW approximation

Using Yambo in Parallel

This modules contains very general discussions of the parallel environment of Yambo. Still the actual run of the code is specific to the CECAM cluster. If you want to run these modules just replace the parallel queue instructions with simple MPI commands.

GW_parallel_strategies_CECAM

Excitons and the Bethe-Salpeter Equation

Yambopy



Modules

Alternatively, users can learn more about a specific runlevel or task by looking at the individual documentation modules. These provide a focus on the input parameters, run time behaviour, and underlying physics. Although they can be followed separately, non-experts are urged to follow them as part of the more structured tutorials given above.

Schools