Guide for JETTO users: interfacing with standalone version of QuaLiKiz
You will find below an updated documentation about:
How to get started
You can find the latest download and installation instruction in the QuaLiKiz repository
To make life easier (no username password verification needed for access), you can upload your SSH key to your GitLab account
- From Freia/JAC. Make a key with "ssh-keygen", type enter enter enter until it's finished.
- Copy the text written in .ssh/id_rsa.pub into "settings”, found when right clicking on your profile on the top right corner of your GitLab screen then “SSH keys". This key should look like
ssh-rsa areallyveryverylongstringwithlotsoflettersandnumbersandsymbols== username@jac...When you copy paste, make sure that the really long string doesn't contain any newlines as a byproduct from the copy-paste.
Interfacing QuaLiKiz stand-alone for JETTO run
Preparing an input file for QuaLiKiz based on a cataloged JETTO run at a given time:
In yourdir/QuaLiKiz-matlabtools, you can find the matlab tools you need to use to read a chosen JETTO run and prepare QuaLiKiz input files. These instructions use the matlabtools. Documentation on the Pythontools will follow. Open matlab, then type
>> run newrun
Choose the name of your new run directory, you will then be automatically put in this new run directory.
You will be asked to give a name to your batch job which you can leave blank, you will then be asked for the pulse number, the JETTO run user ID, its sequence number. You will be asked to choose the time of the analysis. Finally you will have to choose the radial range you want to cover and the number of radial positions at which you want to calculate the unstable mode spectra and the quasilinear fluxes.
A figure displaying the main key parameters for the linear stability allows you to check that the parameters you have been reading are the ones you were expecting.
Sending a QuaLiKiz stand-alone run
You are now ready to send QuaLiKiz calculation on your data. To do so from your run directory on the JACs, type:
mpiexec -np 8 QuaLiKiz.exe (e.g. with 8 cores here, you can also choose 16 cores).
For 25 radial points, 8 wave numbers on 8 processors it will take approximatively 15 sec.
Plotting QuaLiKiz’ s results
Here are the plotted QuaLiKiz results, for the pulse 92436, userid gszepesi, sequence number 1056, at 51 s.:
A summary of the main input data:
The most unstable growth rate vs wave number and x:
The spectra at a given normalized radius:
The energy fluxes:
A check of ambipolarity calculated using the fluxes or using the D and V decomposition:
The particle fluxes, with the various contributions to the convective velocity: