how to make an input file  
^{Micro}^{Stability
code KINEZERO}^{
}
User's
guide
finite Larmor radius and banana width effects corrected !
Kinezero
is a linear local gyrokinetic code used for microturbulence analysis. It is an
eigenvalue code, therefore it can find cohabitating unstable modes, but this
unables it to be extended to a nonlinear version. It uses the ballooning
representation, therefore it stops being valid for very low magnetic
shear. Also it does not include shaping effect, it uses a sa
geometry,
valid for circular crosssection. The
code takes into account for ions and electrons, passing and trapped, this means
that Ion Temperature Gradient modes, Trapped Electron Modes and Electon
Temperature Gradient modes are computed. The impact of collisions on the trapped
electrons are included. The
eigenfunction is an electrostatic potential (no magnetic perturbation included).
A gaussian function is used as a guess for the eigenfunction, this allows
the code to be very fast. Indeed, it runs in about
one hour on one CPU to calculate 150 growth rates, which about 380 times
faster than GS2 ran in the same limit
as kinezero! This rapidity
allows to test extensively the impact of a large variety of parameters on the
microturbulence.
collisionless,
electrostatic, sa geometry,
Z_{eff }= 1:
benchmark based on the ITPA profile database data from the web site: tree = jet, shot = 46664, time = 45.1 s. Input file for GS2 made using Colin Roach's IDL tool: gs2get.pro Input file for kinezero made using the matlab tool described below: mdskize.m 
For more detailed information on the code see: C. Bourdelle, X. Garbet, G. T. Hoang, J. Ongena, R. V. Budny, Nuclear Fusion 42, 892 (2002)
Illustrations of the impact of a large variety of parameters see: slides of the training given at JET in November 2004.
For details on the implementation of collisions see G. Regnoli, M. Romanelli, C. Bourdelle et al, EPS 2005
1. new publications
· impact of density peaking at different collisionalities based on pellet injected discharges in FTU, Michele Romanelli et al , Physics of Plasmas 2004
· impact of the a parameter and its role in ITB sustainement based on ITPA profiles data analysis, Clarisse Bourdelle et al, Nuclear Fusion 2005
· stability analysis of JET ITBs, Yuri Baranov et al, Plasma Physics and Controled Fusion 2005
· stability analysis of JET electron ITBs, G.M.D. Hogeweij et al, EPS 2005
2. few upgrades in the interfacing tools
· Kinezero is now interfaced in JAMS at JET, you can find here the slides presented during the training session at JET in November 2004
3. Large upgrades in the code itself
· The collisions have been added on trapped electrons thanks to Giorgio Regnoli, see his 2005 EPS paper for more details
· The model used for the mode width (w) of the trial eigenfunction has been sensibly improved as can be seen on the figure below showing d/w versus s, for more details read the note.
· As
can be seen on the comparison between Kinezero and GS2 shown in the
mode width discussion, Kinezero gives lower growth rates than GS2. This
difference is due to the way the bounce average of the trapped particles is
treated in both codes. Kinezero
simplified
way of accounting for both the finite Larmor radius effects and for bounce
average has now been modified in order to match better the more exact GS2
approach. Previous qualitative behaviours of the growth rates are not affected,
but their absolute values are now higher and the shape of the spectra is
slightly modified. More details in the note here.
click here to view former updates, 05/03/04
Coming updates :
None forseen at the moment, but suggestions and good will are welcome!
*** *** *** ***
To make an input file you have multiple choices, or you make it from your own data, or you read the ITPA profile database, or you make it using the Jams interface at JET :
1.
To prepare an input
file with your own experimental data but this way of working is quite artisanal
and not appropriate to do runs based on experimental data, it is always better
to work from JETTO or so output:
·
create
a kinezero directory
·
download
prepkize.m or from the JAC at JET copy ~cbourde/kinezero/kizecollflr/prepkize.m
·
create
a matlab file called datajet_11111_030.mat, where 11111 stands for the shot
number and 030 stands for a time label such that 3s is 030, 42.34 s gives 423
and 42.36 gives 424. The file has to include :

B
: the magnetic field in T

a
: the minor radius in m

R
: the major radius in m

x
: the normalized flux surface label (ideally the normalized sqrt of the toroidal
flux, or r/a)

te
: the electron temperature in keV at each x

ti
: the ion temperature in keV at each x

ne
: the electron density in units of 10^19 m^3 (ie for 4.10^19 m^3 should be ne
= 4)

q
: the security factor at each x

zeff
: the effective charge at each x a little smoothing of the profile is advised,
otherwise you will have grad(X)/X that will jump around a bit too much, of
course the big features have to be kept, so it is a delicate exercise.
· then go in matlab and run prepkize.m, it will read the datajet file you just made, and calculate the gradients, the Larmor radii and so on. It is plotting the profiles and the associated grad(X)/X so that you can check if the smoothing was correct. For example, in an ITB, check that grad(X)/X peaks at the barrier location, or on the contrary if grad(X)/X looks very noisy, then the smoothing might have been too light leading to misleading variations of the gradients. You will also have a plot of the electron collision frequencies compared to the electron vertical drift, nw_{ge}, for the minimum n and for n at k_{q}r_{i} = 2, which corresponds more or less to to upper limit of the TEM range.
·
the
file containing all the needed information to run Kinezero is saved in the
current directory, it is called basekinezero_11111_030.mat, where 11111 is the
shot number and 030 is the time label such that 3s is 030, 42.34 s gives 423 and
42.36 gives 424.
2.
From the ITPA database
You just need
to know the tree name ('jet', 'itb_tftr', etc), the shot number you are
interested in and at what time. This program reads data from the
ITPA profile database.
·
create
a kinezero directory
·
download
mdskize.m or copy
from the JAC at JET ~cbourde/kinezero/kizecollflr/mdskize.m
· then go into matlab and run mdskize.m. It will pick up from the profile database the following data: B_{tor}, a, R, and the q, T_{e}, T_{i}, n_{e} and Z_{eff} profiles. It plots the profiles so that you can make sure that it is what you want to analyze. Then it calculates the gradients, Larmor radii and so on it will need in Kinezero. It plots the profiles and the associated grad(X)/X so that you can check if the smoothing was appropriate. For example, in an ITB, check that grad(X)/X peaks at the barrier location, or on the contrary if grad(X)/X looks very noisy, then the smoothing might have been too light leading to misleading variations of the gradients. You will also have a plot of the electron collision frequencies compared to the electron vertical drift, nw_{ge}, for the minimum n and for n at k_{q}r_{i} = 2, which corresponds more or less to to upper limit of the TEM range.
· the file containing all the needed information to run Kinezero is saved in the current directory, it is called basekinezero_11111_030.mat, where 11111 is the shot number and 030 is the time label such that 3s is 030, 42.34 s gives 423 and 42.36 gives 424.
3.
Input from the JETTO
output from the JAC machines at JET:
You just need to know which shot
number you are interested in and at what time. This program reads JETTO output, so you need to give
the JETTO run user ID and sequence number of the shot you want to analyze.
·
create
a kinezero directory
·
download
jettokize.m or from the JAC at JET copy
~cbourde/kinezero/kizecollflr/jettokize.m
· then go into matlab and run jettokize.m. It will pick up the JETTO Btor, a, R, and the q, Te, Ti, ne and Zeff profiles. It plots the profiles so that you can make sure that it is what you want to analyze. Then it calculates the gradients, Larmor radii and so on it will need in KINEZERO. It plots the profiles and the associated grad(X)/X so that you can check if the smoothing was appropriate. For example, in an ITB, check that grad(X)/X peaks at the barrier location, or on the contrary if grad(X)/X looks very noisy, then the smoothing might have been too light leading to misleading variations of the gradients. You will also have a plot of the electron collision frequencies compared to the electron vertical drift, nw_{ge}, for the minimum n and for n at k_{q}r_{i} = 2, which corresponds more or less to to upper limit of the TEM range.
· the file containing all the needed information to run Kinezero is saved in the current directory, it is called basekinezero_11111_030.mat, where 11111 is the shot number and 030 is the time label such that 3s is 030, 42.34 s gives 423 and 42.36 gives 424.
·
download
kizecollflr.targz, then in unix: cp kizecollflr.targz kizecollflr.tar.gz and gunzip
kizecollflr.targz and tar
xvf kizecollflr.tar. In the makefile, correct
if necessary the links to the following libraries :
libnag.a and libmat.so. Or copy from the JAC at JET in your kinezero directory
~cbourde/kinezero/kizecollflr/*.f90, makefile, *.a, *.m, kinezero.cmd
·
type "make", now the
executable of Kinezero is ready
·
then addapt the kinezero.cmd batch
file by: changing 11111 by the shot number, 030 by your time label, change also
"cbourde" by your own user name, make sure the directory you are
sending the output is correct and set your email address so that
you will recieve an email when the run has completed. If you want to send many
jobs at the same time, save kinezero.cmd with a
different label, for example kize_11111_031.cmd.
· then type: llsubmit kize_11111_030.cmd  to check if your job is running do : xloadl & then wait for the email that will tell you when it is completed. If your local batch system is different from the JAC system at JET, adapt this ".cmd" file and the submition command following the recommandations of your system manager.
· dowload plotkize.m or plotkize_omeb.m
·
in matlab,
type "plotkize", then it
will ask you the shot number and the time. The 1st plot is the maximum growth
rates, among the different unstable branches, versus x and the wave numbers. The
matching real parts of the frequencies are also plotted in 3D, it allows to
check the signs: negative means in the ion drift direction, therefore "ITG
dominated", positive means in the electron drift direction, therefore
"TEM dominated" or pure ETG at high wave number (n > 100). The 3rd
and 4th plots are the maximum growth rates for k_{q}r_{i} < 2 (ITGTEM
range) and the maximum for k_{q}r_{i} > 2 (ETG range)
versus x, accompanied by an evaluation of the contribution of trapped/passing
ions/electrons in the power exchange of the most unstable mode at each radial
position. Then it will ask you at what radius you want to plot the a spectrum of
modes. Of course you can and should adapt this plotting tool to your convenience.
If you have a file named omExB_11111_060.mat created with mdskize.m, then you can use plotkize_omeb.m. It will also plot the ExB shearing rate read in the database with the ITGTEM growth rates. Do not forget to check carefully how was calculated the ExB shearing rate: toridal velocity profile measured or not, etc.
C. Bourdelle, X. Garbet, G. T. Hoang, J. Ongena, R. V. Budny, Nuclear Fusion 42, 892 (2002)
C Fourment, G T Hoang, et al Plasma Physics and Controlled Fusion 45, 233 (2003)
Michele Romanelli et al , Physics of Plasmas 2004
Clarisse Bourdelle et al, Nuclear Fusion 2005
That should be it,
for more information and help
please contact Clarisse Bourdelle : mailto:clarisse.bourdelle@cea.fr , +33 (0)4 42 25 61 36.