This page lists some of the diagnostics available to JOREK users. This list is far from complete, and you can help by expanding it.
Diagnostics
There are a lot of diagnostics available for JOREK. Some of the most important:
| Program | Description |
|---|---|
| jorek2vtk(_3d) | Convert jorek_restart.rst files to VTK files |
| jorek_read_h5 | Python script for reading HDF5 files to VTK objects and files |
| jorek2vtk_gaussvortterms | Calculates the different terms of the vorticity equation integrated in the Gaussian points and creates a VTK file where the different terms can be visualized in the poloidal plane. |
| jorek2_four | Perform a two-dimensional Fourier analysis of the jorek_restart.rst file |
| jorek2_poincare | Create a Poincaré plot for a JOREK restart file |
| jorek2_postproc | The diagnostic program jorek2_postproc is a very flexible diagnostic tool that can be used interactively or using small scripts |
| jorek2_diagno | Extracts some useful data from a JOREK restart file |
| jorek2_diagno_spi | Extracts some useful data from a JOREK restart file, including the SPI fragments position and radius at the time of the restart file |
| jorek2_connection2 | This diagnostic produces a poincaré plot of the magnetic field geometry |
| jorek2_connection_flux_aligned | Calculates connection length to the simulation boundary and the corresponding strike points of field lines on n=0 flux surfaces |
| jorek2_fields_xyz | Calculates B_x, B_y, B_z at given (x,y,z) cartesian coordinates |
| jorek2_wall_forces | Calculates the total wall forces (F_x, F_y, F_z). It needs JOREK-STARWALL |
| jorek2_fast_camera | This diagnostic produces a camera image of the visible plasma (Dalpha) |
| rst_bin2hdf5 & rst_hdf52bin | Convert jorek_restart.rst to jorek_restart.h5 and vice-versa. |
| plot_live_data.sh | Plot several 0D quantities as the simulation runs (gnuplot) |
| Diagnostic Framework new_diag | Allows to evaluate arbitrary physical expressions (current list of expressions) at arbitrary positions in the computational domain either in JOREK units or in SI units. This framework is used by the jorek2_postproc diagnostics for most of its functionality, but even more powerful diagnostics can easily be written on top of the framework. |
| radiation_function_diagno | Output the radiation power function for the hard-coded impurity under hard-coded parameters |
| jorek2_fieldlines_vtk_newdiag | This diagnostic evaluates arbitrary physical expressions (using the new_diag framework) along field lines and writes this information to both vtk and txt files |
| jorek2_solcurrent | This diagnostic postprocesses jorek_restart.h5 to determine scrape-off layer currents (thermo-electric current between target plates) by solving Stangeby eq. 17.29 |
The diagnostics tools should have been compiled with the same hard-coded parameters as JOREK.
To run diagnostics on Marconi, you may need to book a debug node with a command of the type:
salloc --nodes=1 --time=01:00:00 --exclusive --account=FUA36_MHD --partition=skl_fua_dbg
To run diagnostics on Leonardo DCGP, you may need to book a debug node with a command of the type:
salloc --nodes=1 --time=10:00 --account=FUA38_MHD_0 --partition=dcgp_fua_dbg
and run:
srun jorek2_diagno < jorek_in
Alternatively you can run directly on the login node by first setting the ulimit memory limit to unlimited with:
ulimit -s unlimited
Scripts
A couple of scripts are available in the folder trunk/util/:
| Script | Description |
|---|---|
| config.sh | List or modify hard-coded parameters |
| plot_live_data.sh | Plot time-traces of energies or growth rates (and more) while a simulation is running or afterwards |
| plot_grids.sh | Plot the grid to a file or the screen |
| plot_live_data.py | Python version of plot_live_data.sh |
| read_jorek_logfile.py | Search JOREK logfile for specific variable |
| plot_mlog.py | Plot memory usage |
Output files
During a run some output files are generated. This is a short summary of the different files.
- macroscopic_vars contains a list of the energies and growth rates in the simulation (and various other quantities)
jorek00XXX.rstare snapshots that can be used to restart the simulationboundary.txtequilibrium.txtgrid_fluxsurface.datgrid_initial.dat- jorek2.ps is generated at the end of the simulation and contains some plots of the energies and magnetic field.
qprofile.datspecial_equilibrium_points.datT_rho_profiles.dat