It enables effective and efficient computation of weight functions using the Julia programming language (coupled to other programming languages, e.g. Python). As of the current version (v1.2.0), the OWCF can compute the following types of weight functions:
- Orbit-space weight functions. Computed using the guiding-centre computational framework (GCCF)(written in the Julia language) developed by Luke Stagner with additions by Henrik Järleblad. The GCCF is comprised of the Julia packages EFIT.jl, Equilibrum.jl, GuidingCenterOrbits.jl and OrbitTomography.jl. The OWCF computes fast-ion orbits in the (E,pm,Rm) orbit space, and feeds them as weighted (E,p,R,Z) data into the forward model of your choice.
- Velocity-space weight functions. Computed by feeding (E,p) points into a synthetic diagnostic code of your choice, while keeping (R,z) constant. It can output and save the 2D weight functions in both (E,p) and (vpara,vperp).
The OWCF also has the ability to compute simple forward model signals. This can be done via the script calcSpec.jl (but not directly, please utilize a start script). In fast-ion tomography, the main equation is
S = WF
where S is the forward model (or experimental) signal, W is the weight function that captures all of the forward model into a simple matrix, and F is the fast-ion distribution reshaped as a vector. To clarify, the OWCF thus has the ability to compute both S and W (both not F). F needs to be provided as e.g. a TRANSP distribution, put into .jld2-format via getEpRzFIdistrFromTRANSP.jl, and then transformed to orbit space via ps2os.jl. You can also create your own fast-ion distribution in (E,p,R,z) or (E,pm,Rm) formats. As long as you save the fast-ion distribution with the same keys as required by e.g. ps2os.jl, it will be usable.
The OWCF_manual.pdf contains more detailed, and likely more up-to-date, information than this simple README. Please consult the OWCF_manual.pdf document for more information on the OWCF. More information about the OWCF can also be obtained by reading the following publication:
H. Järleblad et al, A framework for synthetic diagnostics using energetic-particle orbits in tokamaks, Comp. Phys. Comm. 294, 108930 (2024)
- For Windows, please follow the steps in howToInstallJuliaAndTheOWCF_Windows.pdf.
- For Mac, please follow the steps in howToInstallJuliaAndTheOWCF_Mac.pdf
I highly recommend you read one of those .pdf documents before trying to install the OWCF. If you really want to install the OWCF in a quick-and-dirty-and-risky way, do the following
navigate to the OWCF folder using a terminal
julia
using Pkg
Pkg.activate(".")
ENV["PYTHON"] = "...path to your Python executable..."
Pkg.add("PyCall")
ENV["PYTHON"] = "...path to your Python executable..." # Often redundant
Pkg.build("PyCall")
] instantiate
wait for a long time
Done!
To use the OWCF, find out which script you need. Copy the template start file from the templates/ folder into the main OWCF/ folder. Specify the required inputs. Execute. Get your output results file. Visualze the results using any of the OWCF apps in apps/ or via a plot function in extra/gui.jl Or manually, by writing the necessary code in e.g. scratch.jl.
Some scripts are executed without a template file. The input variables are then specified by modifying the script directly.
If executing on a SLURM computational cluster, copy the .sh submit template you need from templates/ into the main OWCF/ folder. Modify it as needed. Specify the same number of CPU cores in the start file. Submit to the workload manager.
- The DRESS code [J. Eriksson et al, Comp. Phys. Comm., 199, 40-46, 2016]
The DRESS code is a code for computing the energy and momentum of fusion reaction products, given the collision and fusing of two reacting nuclei. It also has the possibility to load, handle and use TRANSP data. Given a fusion reaction, it computes the resulting energy spectrum of the emitted particle (e.g. neutrons, gammas). It incorporates diagnostic lines-of-sight via the input of data from the LINE21 code. The DRESS code is modular in the sense that any two-body fusion reaction can be added to the code, simply via defining the corresponding cross-sectional data. As of this version of the OWCF and DRESS code, the DRESS code can only compute one-step fusion reactions. To upgrade the OWCF and DRESS code to be able to handle two-step fusion reactions, it is supposed that the files fusreact.py, relkin.py and relscatt.py would need to be upgraded to compute a second, random step. Where the product particle of interest moves a short random distance in (R,phi,z), and then de-excites (or similar) and releases a gamma-photon (for example).
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.eqdsk/.geqdsk files. These kind of files are used as input files to TRANSP. They contain information about the magnetic flux function and the tokamak geometry (first wall, divertor etc). For a full breakdown of what an .eqdsk/.geqdsk file usually contains, and its structure, please examine the misc/eqdsk_file_breakdown.pdf file.
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.jld2 file. If the magnetic equilibrium is specified with a .jld2 file, as of the current version of the OWCF (v1.2.0), it has to be an output file of the extra/compSolovev.jl script. Or have an equivalent structure and data content. The compSolovev.jl script provides the possibility to create customized Solov'ev magnetic equilibria.
- TRANSP shot files. They are usually saved on the form XXXXXAXX.cdf where 'X' can be any (different) numbers and 'A' any letter. E.g. 94701V01.cdf, or 99965K71.cdf. These files is essentially the output file of the TRANSP run with the same ID (e.g. 94701V01). They contain a multitude of data (hence, they are usually quite large) and the OWCF only needs them for their thermal plasma density and temperature profiles (used by the DRESS code).
- TRANSP fast-ion shot files. They are usually computed using the NUBEAEM module of TRANSP. These files contain the expected fast-ion distributions for the time points of interest. They contain fast-ion data but also time window information data that the OWCF uses to select the corresponding thermal plasma density and temperature profiles. These kind of files can be provided as input to the extra/getEpRzFIdistrFromTRANSP.jl script, which will convert it to a .jld2 file with the fast-ion specified on a regular (E,p,R,z) grid.
- LINE21 (is that actually the name of the company?) output files. These have diagnostic viewing cone data organized into columns. The columns are, in order: x, y, z, c (angular weight), volume, ux (x component of vector pointing towards the detector at the given x,y,z position), uy, uz, R, phi, solid angle. Talk to Massimo Nocente or Jacob Eriksson to acquire LINE21 files for diagnostic viewing cones.
- Create custom LOS. The user can use the extra/createCustomLOS.jl script to create a custom LOS of their own. This can be done in several different ways and the reader is referred to the description at the start of the createCustomLOS.jl script for a detailed discussion. The output file will be a .txt file identical in structure to a LINE21 file.
- No viewing cone. If no viewing cone file is specified, sperical emission is assumed (4*pi s.r.)
- calc2DWeights.jl. Compute two-dimensional velocity-space weight functions for an (E,p) grid, at a given (R,z) point of the plasma.
- calcEpRzTopoMap.jl. Compute orbit-type topological maps for a (E,p,R,z) grid. Including maps of poloidal and toroidal transit times, if requested.
- calcOrbWeights.jl. Compute orbit weight functions, and save them as an orbit weight matrix. Use the DRESS code or simply compute and bin projected velocities if requested.
- calcSpec.jl. Compute the expected synthetic diagnostic signal spectrum, given a fast-ion and thermal plasma distribution.
- calcTopoMap.jl. Compute orbit-type topological map for a (E,pm,Rm) grid. Include maps of poloidal and toroidal transit times, if requested.
- ps2os.jl. Transform a fast-ion distribution from (E,p,R,z) space to (E,pm,Rm) space. Save as a 1D compressed vector, and also as a 3D data array if requested.
- ps2WF.jl. Compute WF signals with abtrirarily high grid resolution in (E,pm,Rm) space. Also compute orbit splits of W, F and WF if requested.
- comWebApp.jl. A simple app that lets the user visualize a Solov'ev magnetic equilibrium and fast-ion orbits. The Solov'ev equilibrium can be customized interactively and the orbit(s) can be changed by changing (E,mu,Pphi; sigma) coordinate values. The app will then re-compute new orbits and magnetic equilibria in real-time.
- distrWebApp.jl. An app that lets the user visualze a (E,pm,Rm) fast-ion distribution in terms of fast-ion energy slices. The user can also choose to input a second fast-ion distribution, and the two will then be able to be compared interactively.
- EpRzWebApp.jl. An app that lets the user visualize orbit topological maps in (E,p,R,z) coordinate space. The option to also visualize poloidal and toroidal transit times exists. The user can also choose to input a fast-ion distribution in (E,p,R,z) format. The app will then superimpose topological boundaries and the fast-ion distribution can be visualzed via a toggle button.
- modeAnalysisWebApp.jl. An app that lets the user visualize simple MHD mode resonances in (E,pm,Rm) orbit space. The user can interactively explore different energies, mode numbers and frequencies. Only toroidal (n) and poloidal (m) mode numbers are included. (E,mu,Phi;sigma) space can be accessed via a toggle button.
- orbitsWebApp.jl. It is arguably the flagship app of the OWCF. It lets the user visualize fast-ion orbits interactively via a topological map in (E,pm,Rm) space. Maps for poloidal and toroidal transit times can also be included. The user can switch to (E,mu,Pphi;sigma) space via a toggle button.
- orbitWebApp.jl. A simple app that lets the user visualize a single fast-ion orbit in detail. The endpoint of the orbit can be changed interactively. The coordinate space is (E,pm,Rm).
- signalWebApp.jl. An app that lets the user visualze a WF signal and orbit splits of WF, W and F, together with their dependence on E, pm and Rm, respectively. Log-scales, splitting, fractions and more options can be changed interactively via toggle buttons.
- weightsWebApp.jl. An app that lets the user interactively visualize the orbit weight functions of an orbit weight matrix. The diagnostic measurement bin and fast-ion energy slice of interest are changed via sliders. A WF signal, an S signal, a fast-ion distribution and null orbits can all be optionally included. The weight visualization can be switched to (E,mu,Pphi;sigma) via a toggle button. Diagnostic viewing cones can be optionally included.
- weightWebApp.jl. Please notice, no 's'. This app lets the user visualize the expected diagnostic signals of fast-ion orbits. The (E,pm,Rm) is navigated interactively via sliders and a topological map. Diagnostic viewing cones can be optionally included.
- calcOrbGrid.jl. Compute an orbit grid and save it, and the valid orbits, as an easily loadable .jld2 file, for the other OWCF scripts to use.
- calcOrbSpec.jl. Keep track of the functions that compute expected synthetic diagnostic spectra given a fast-ion orbit.
- extractNullOrbs.jl. Take a diagnostic signal and an orbit weight matrix in 2D form, and identify the null orbits, given thresholds.
- extractTempDens.jl. Take TRANSP data and extract the thermal plasma density and temperature profiles.
- extractTopoBounds.jl. Take a topological map and examine it to locate the boundaries between topological regions. Save the topological boundaries as a .jld2 file.
- F_os_1Dto3D.jl. Inflate a fast-ion distribution in its compressed 1D form into its full 3D form.
- orbweights2Dto4D.jl. Inflate an orbit weight matrix from its compressed 2D form into its full 4D form, set by the user.
- orbWeights4Dto2D.jl. Take an inflated orbit weight matrix in its 4D form, and compress it into its 2D form.
- os2com.jl. A script that can be used to transform quantities from (E,pm,Rm) orbit space to (E,mu,Pphi;sigma) constants-of-motion space.
- compSolovev.jl. Compute a Solov'ev magnetic equilibrium and first wall geometry, based on the inputs. Save as .jld2 file.
- createCustomLOS.jl. This script will help the user create a custom line-of-sight (LOS) file, usable by the OWCF. The file format mimics the file format used by the LINE21 code. The options for the custom LOS includes detector position, angle and size. A cylinder shape is assumed for the LOS.
- dependencies.jl. A collection of many functions used by various parts of the OWCF.
- getEpRzDistrFromTRANSP.jl. Given a TRANSP fast-ion distribution file and user-requested (E,p,R,z) grid, compute the fast-ion distribution on that grid. Save as .jld2 file.
- gui_appendix.jl. Some extra plotting function, almost never used by users of the OWCF.
- gui.jl. A collection of functions that can be used to plot various quantities computed by the OWCF.
- availReacts.jl. Keep track of the fusion reactions availabe for simulation by the OWCF, through the DRESS code.
- diag2tokamak.jl. A (collection of) function(s) that keeps track of which diagnostics are installed at which tokamaks.
- rewriteReacts.jl. A collection of functions that provides the utility to re-write the notation of fusion reactions in different formats.
- species_func.jl. A collection of functions that provide easy access to the properties of various ion species.
- temp_n_dens.jl. Store and provide default thermal plasma temperature and density profiles for the OWCF. Also includes loading and interpolation functions for TRANSP thermal temperature and density data.
Other data in the misc/ folder includes: default_temp_n_dens.png, eqdsk_file_breakdown.pdf, howToLoadFromTRANSP_FI_CDF.jl and transp_outputs.txt.
If you would like to use the OWCF on a SLURM computational cluster, you can use the .sh submit file templates to easily submit OWCF runs for batch jobs.
Good luck! Please consult the OWCF_manual.pdf, howToInstallJuliaAndTheOWCF_MacOS.pdf and howToInstallJuliaAndTheOWCF_Windows.pdf documents for further info.
Henrik Järleblad A (not-so) tired (anymore) postdoc December 14th, 2023
