ECRad

Toolkit for the forward modeling of electron cyclotron emission measurements. Comes with three modules: ECRad_core, the Fortran90 radiation transport model, ECRad_GUI a graphical interfance for the model and ECRad_PyLib which provides an API to call ECRad from other codes.

ECRad

Installation

ECRad is distributed through conda/mamba. Please check these instructions on how to install miniforge.

It is recommended to install through mamba over conda because mamba has much improved environment solving. ECRad is available for python 3.10 and python 3.11.

With mamba installing ECRad is as simple as: For python 3.8

mamba create -n ECRad python=3.8 ecrad_gui

For python 3.10

mamba create -n ECRad python=3.10 ecrad_gui

For python 3.11

mamba create -n ECRad python=3.11 ecrad_gui

and then activate the environment via:

conda activate ECRad

IMAS support

Even when installed through mamba ECRad can use a system IMAS installation. To do so load IMAS first then activate the ECRad conda environment. If the IMAS python library directory is in your $PYTHONPATH and you have matched the major version of python between the two environments (i.e. both use python 3.8) then it should work.

Using ECRad

Unfortunately there is no detailed user-guide at the moment. Below there is a rough sketch of a typical workflow. Some information can also be found in this article. If you don't have access to it please contact me and I will send you a pre-print.

The easiest way to use ECRad is through its GUI. It also has APIs for python, Fortran and Muscle3 applications/workflows. These are more difficult to use, and they need to be treated on a use-case basis.

Starting the GUI

Once the conda/mamba environment has been activated (see Installation) simply type

ecrad_gui

into your shell. The GUI should show up.

Loading data

ECRad supports IMAS and OMAS for IO. You can also manually prepare data, please check out this example code for more info.

The following fields in the IMAS schema are mandatory:

equilibrium:
  - equilibrium.time_slice.:.profiles_2d.grid.0.dim1
  - equilibrium.time_slice.:.profiles_2d.grid.0.dim2
  - equilibrium.time_slice.:.profiles_2d.grid.0.psi
  - equilibrium.time_slice.:.profiles_2d.grid.0.Br
  - equilibrium.time_slice.:.profiles_2d.grid.0.Bt
  - equilibrium.time_slice.:.profiles_2d.grid.0.Bz
  - equilibrium.time_slice.:.global_quantities.psi_axis
  - equilibrium.time_slice.:.global_quantities.psi_boundary

wall:
  - wall.description_2d.0.limiter.unit.0.outline.R
  - wall.description_2d.0.limiter.unit.0.outline.z

ece:
  - ece.channel.:.frequency.time
  - ece.channel.:.frequency.data
  - ece.channel.:.if_bandwidth
  - ece.line_of_sight.first_point.r
  - ece.line_of_sight.first_point.phi
  - ece.line_of_sight.first_point.z
  - ece.line_of_sight.second_point.r
  - ece.line_of_sight.second_point.phi
  - ece.line_of_sight.second_point.z

If all of this data is present in the form of an ODS or IDS you can load it by going to through the corresponding Load from IMAS database and Load from OMAS buttons. You can also load scenarios from previous ECRad runs via the Load ECRadScenario button.

Note that for OMAS loading from the machines database is only supported for DIII-D.

Once you load from either OMAS or IMAS you must pick whether the time base from equilibrium or core_profiles is to be used. Ideally these time bases should be identical, otherwise nearest neighbor interpolation will be used.

Once the scenario data has been loaded, the diagnostic data has to be loaded by selecting the diagnostic configuration tab. Here you can either manually enter diagnostic data, or again load from IMAS or OMAS. Again you can also load previous results via the Load launch from ECrad result/scenario button.

Once both plasma scenario and launch configuration is set you need to move on to the ECRad configuration tab.

Configuring ECRad

Please refer to the CPC article for details on the options.

In principle there is only few options you will need to touch:

Working dir This is where any results will be stored
Scratch dir Set this to the same folder as Working dir. It is intended to be used in conjunction with SLURM submission but this feature is not maintained at the moment.
For most cases you want Extra output checked.
For most cases you want to check Parallel and uncheck debug and Batch
For number of cores please pick a number appropriate for your machine. It should be at most the number of physical number of cores.
Neither walltime nor memory matter if batch submission is not used.

Running ECRad

Once everything is set, simply press the Start ECRad button up top and ECRad should start. Note that the output from ECRad is not parsed to the log box due to technical limitations, and the ECRad output will appear in the shell you used to start the GUI.

Inspecting the outputs

The GUI will save all outputs to a NetCDF file for further processing. You can inspect the entire content of this file in the Misc. Plot tab.

To plot something you first select what should be plotted on the y axis of the plot. For this first you select a y-group:

Trad refers to quantities that are line integrated such as the radiation Temperatures or the optical depth.
resonance This field is usually used for x axis quantities. It includes cold/warm resonances in various coordinates
ray These are quantities that are used somewhere in the calculation of Trad. Of particular interest are R and z for plotting the line of sight.
BPD This tab is the birthplace distribution. It breaks down how each point on the line of sight contributes to the measurement.
weights The only quantity of general interest here is mode_frac which indicates the X-mode content of the measurement.

Once a y group has been selected the x-group and y quantity can be chosen. One of the most classic combinations would be:

y group
- Trad
y quantity
- Trad
x group
- resonance
x quantity
- rhop_cold

In addition it is also possible to plot some of the scenario information using the box Add scenario quantity to plot. It uses both y-axes and combines radiation and electron temperatures. So for the above selections it is possible to select

Te
ne

by clicking the corresponding fields while holding the shift key.

For R-z plots it can be useful to select rhop from this box, which then shows the flux surfaces as contours. In this case it is worthwhile to also check the Equal aspect ratio box.

License

MIT

AreWeDreaming/ECRad