Tutorials: Difference between revisions
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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. | ||
====Introduction==== | ====Day 1: Introduction==== | ||
* [[First steps: a walk through from DFT to optical properties]] | * [[First steps: a walk through from DFT to optical properties]] | ||
====Quasiparticles in the GW approximation==== | ====Day 2: 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]] | ||
====Using Yambo in Parallel==== | ====Day 3: 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 | ||
* [[GW_corrections_for_diamond|GW on diamond]]: use Yambo in parallel to converge a GW calculation for diamond | * [[GW_corrections_for_diamond|GW on diamond]]: use Yambo in parallel to converge a GW calculation for diamond | ||
====Excitons and the Bethe-Salpeter Equation==== | ====Day 4: 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]] | ||
| Line 85: | Line 85: | ||
<!--* [[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==== | ====Day 5: Yambo-python driver==== | ||
* [[First steps in Yambopy]] | |||
*[[First steps in Yambopy]] | * [[GW tutorial. Convergence and approximations (BN)]] | ||
* [[Bethe-Salpeter equation tutorial. Optical absorption (BN)]] | |||
*[[GW tutorial. Convergence and approximations (BN)]] | |||
*[[Bethe-Salpeter equation tutorial. Optical absorption (BN)]] | |||
* [http://yambopy.readthedocs.io/en/devel/tutorial.html Efficient many body calculations with the Yambo-python tool] | * [http://yambopy.readthedocs.io/en/devel/tutorial.html Efficient many body calculations with the Yambo-python tool] | ||
<!--* [[How to obtain the absorption spectrum of a bulk material: h-BN]] - this would basically be a list of links of particular modules --> | <!--* [[How to obtain the absorption spectrum of a bulk material: h-BN]] - this would basically be a list of links of particular modules --> | ||
Revision as of 13:22, 25 April 2017
Tutorial files and use of CECAM cluster
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.
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 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.
Next you must log into the linux cluster directly, using the node node0RS that is 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 set DISPLAY:0.0 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 gnuplot> set terminal dumb.
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.
Next move into the bellatrix cluster via:
ssh -Y cecam.schoolXY@cecampc4.epfl.ch
replacing XY with the appropriate number.
This cluster is equipped with 16-core nodes based on Intel processors.
The Unix environment (already set by default), can be obtained by loading the following modules:
module load gcc/5.3.0 module load openmpi/1.10.2
A tutorial-dedicated queue (cecam_course) allows participants to access up to 20 nodes.
In order to submit to this queue use:
srun -N 2 -n 8 --reservation=cecam_course job.sh
where job.sh is a submission script. In the example above, 2 nodes are requested with -N, together with 8 total MPI tasks (4 per node), and, implicitly, OMP_NUM_THREADS is set to 4 (in order to fill each node with 16 threads).
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.
Day 1: Introduction
Day 2: Quasiparticles in the GW approximation
Day 3: Using Yambo in Parallel
- Parallel GW: strategies for running Yambo in parallel
- GW on diamond: use Yambo in parallel to converge a GW calculation for diamond
Day 4: Excitons and the Bethe-Salpeter Equation
- Calculating optical spectra including excitonic effects: a step-by-step guide
- Obtaining a converged optical spectrum
- Many-body effects in low-dimensional systems: numerical issues and remedies
- Analysis of excitonic spectra in a 2D material
Day 5: Yambo-python driver
- First steps in Yambopy
- GW tutorial. Convergence and approximations (BN)
- Bethe-Salpeter equation tutorial. Optical absorption (BN)
- Efficient many body calculations with the Yambo-python tool
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.
Other stuff and old stuff
- Parallelization
- Yambopy
- GW (quick port just for demo purposes)
- Parallelization (quick port just for demo purposes)
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