Tutorials: Difference between revisions

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[[Instructions for CECAM students]]
[[Instructions for CECAM students]]
The tutorials will be run on the CECAM linux ''cluster''.
* If connecting from the CECAM iMac, your username is indicated on the terminal (''tutoXY'').
* If connecting from your notebook, choose a username [[CECAM accounts 2017|from this list (link)]]
=== Standard tutorials: cecampc4 cluster ===
Log into the cluster via:
ssh -Y tutoXY@cecampc4.epfl.ch
replacing ''XY'' with the appropriate number.
<!--, and find your allocated username ''tutoXY'' and node ''node0RS'' from [[CECAM-accounts-2017|this table]]. -->
Next you '''must''' log into the linux cluster directly, using the node ''node0RS'' that is [[CECAM accounts 2017|associated with the username (link)]], and set up the tutorial as follows:
$ ssh -Y node0RS
$ pwd
/nfs_home/tutoXY
$ which pw.x yambo
/nfs_home/tutoadmin/bin/pw.x
/nfs_home/tutoadmin/bin/yambo
$ cd /home/scratch/                ''(NB: do '''not''' run on the /nfs_home partition!)''
$ mkdir yambo_YOUR_NAME            ''(there are more participants than accounts!)''
$ cd yambo_YOUR_NAME
$ cp /nfs_home/tutoadmin/yambo-2017/tutorials/hBN.tar.gz .
$ cp /nfs_home/tutoadmin/yambo-2017/tutorials/hBN-2D.tar.gz  .
$ tar -zxvf hBN.tar.gz
$ tar -zxvf hBN-2D.tar.gz 
$ ls
YAMBO_TUTORIALS
If you used "ssh -Y", X-forwarding, for plotting with gnuplot, ''should'' work. If not, try <code>set DISPLAY:0.0</code> on your local machine; it might also help to keep one terminal open for plotting and the other for running codes. If all else fails, try the cool gnuplot trick <code>gnuplot> set terminal dumb</code>.
=== Parallel tutorial: bellatrix cluster ===
This cluster is equipped with 16-core nodes based on Intel processors.
A tutorial-dedicated queue (''cecam_course'') allows participants to access up to 20 nodes.
First log into the cecam4 cluster via:
$ ssh -Y tutoXY@cecampc4.epfl.ch
replacing ''XY'' with the appropriate number.
<!--, and find your allocated username ''tutoXY'' and node ''node0RS'' from [[CECAM-accounts-2017|this table]]. -->
Next move into the bellatrix cluster via:
$ ssh -Y cecam.schoolXY@bellatrix.epfl.ch
$ cd /scratch/${USER}                (NB: do not run in the /home folder!)
$ mkdir yambo_YOUR_NAME              (there are more participants than accounts!)
$ cd yambo_YOUR_NAME
replacing ''XY'' with the appropriate number.
This cluster is equipped with 16-core nodes based on Intel processors.
The Unix intel environment can be obtained by loading the following modules:
module purge
module load intel/16.0.3
module load intelmpi/5.1.3
module load python
A tutorial-dedicated queue (''cecam_course'') allows participants to access up to 20 nodes.
In order to submit to this queue you will use a submission script ''run.sh'' you will find in the tarball provided for the tutorials.


== Full tutorials ==  
== Full tutorials ==  
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Each tutorial is fairly standalone, although some require that you have completed previous ones.
Each tutorial is fairly standalone, although some require that you have completed previous ones.


====Day 1: Introduction====
====Introduction====
* [[First steps: a walk through from DFT to optical properties]]
* [[First steps: a walk through from DFT to optical properties]]
====Day 2: Quasiparticles in the GW approximation====
====Quasiparticles in the GW approximation====
* [[How to obtain the quasi-particle band structure of a bulk material: h-BN]]
* [[How to obtain the quasi-particle band structure of a bulk material: h-BN]]
====Day 3: Using Yambo in Parallel====
====Using Yambo in Parallel====
* [[GW_parallel_strategies|Parallel GW]]: strategies for running Yambo in parallel
* [[GW_parallel_strategies|Parallel GW]]: strategies for running Yambo in parallel
* [[Pushing_convergence_in_parallel|GW convergence]]: use Yambo in parallel to converge a GW calculation for a layer of hBN (hBN-2D)
* [[Pushing_convergence_in_parallel|GW convergence]]: use Yambo in parallel to converge a GW calculation for a layer of hBN (hBN-2D)


====Day 4: Excitons and the Bethe-Salpeter Equation====
====Excitons and the Bethe-Salpeter Equation====
* [[How to obtain an optical spectrum|Calculating optical spectra including excitonic effects: a step-by-step guide]]
* [[How to obtain an optical spectrum|Calculating optical spectra including excitonic effects: a step-by-step guide]]
* [[How to choose the input parameters|Obtaining a converged optical spectrum]]  
* [[How to choose the input parameters|Obtaining a converged optical spectrum]]  
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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-->


====Day 5: Yambo-python driver====
====Yambo-python driver====
* [[First steps in Yambopy]]
* [[First steps in Yambopy]]
* [[GW tutorial. Convergence and approximations (BN)]]
* [[GW tutorial. Convergence and approximations (BN)]]

Revision as of 13:17, 2 May 2017

Tutorial files

To follow the tutorials, you must first download or copy data files for each system. Files are distributed as gzipped tarballs. Always extract the tarballs in the same place.
Available systems are: hBN.tar.gz, hBN-2D.tar.gz. You will need both hBN and hBN-2D tarballs.

Instructions for CECAM students

Full tutorials

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. Each tutorial is fairly standalone, although some require that you have completed previous ones.

Introduction

Quasiparticles in the GW approximation

Using Yambo in Parallel

  • Parallel GW: strategies for running Yambo in parallel
  • GW convergence: use Yambo in parallel to converge a GW calculation for a layer of hBN (hBN-2D)

Excitons and the Bethe-Salpeter Equation

Yambo-python driver

Modules

An alternative way to learn Yambo is through a more detailed look at our documentation modules. These provide a focus on the input parameters, run time behaviour, and underlying physics behind each yambo task or runlevel. Although they can be followed separately, they are better followed as part of the more structured tutorials given above.