How-to Guides

Todo

These how-to guides give an overview of how to accomplish different tasks with pyrokinetics, and signpost the user towards more detailed documentation

How do I…?

• Convert input files from code A to code B
• Field line following and Poincaré maps
  • Basic usage
  • Plotting a Poincaré map
  • Field line integration
  • Magnetic field from the vector potential
  • Parallel vector potential
  • Final field line equation
  • Additional diagnostics
• Field line tearing parameter
  • Field line distance element
  • Weighted field-line displacement
  • Physical interpretation
  • Implementation
    • Radial diffusion coefficient
    • Radial displacement
    • Magnetic field correlation length
  • Summary
• Reading and plotting linear outputs
  • Saving and loading NetCDF files
• Merge (multiple) species into a base species
• Normalisation conventions
• Using Units
• Reference values
• Outputs
• Code-specific conventions
  • Pyrokinetics default choice
  • Summary of code conventions
  • Conversion to and from SI units (contexts)
• Perform a N-D scan in parameters A,B,C etc.
  • Simple 1-D scan
  • Running/Submitting simulations
  • Analysing output
  • Higher dimensional scans
  • Bespoke parameters/functions
• Generate an input file from equilibrium and profiles
• Reading and plotting nonlinear outputs
  • Saving and loading NetCDF files
    • Downsampling Data to Reduce Memory Usage
• Real-space reconstruction and 3D flux-tube plotting
  • Loading nonlinear field data
  • Ensuring periodicity in θ
  • Inverse Fourier transform to (x, y)
  • Constructing flux-surface geometry
  • Mapping between y, α and ζ
  • Mapping y → α
  • Relation between α and ζ
  • Physical interpretation
  • Building a 3D toroidal grid
  • 3D visualisation
  • Interpolating onto prescribed (R, Z, φ)
  • Summary
• Read and write different stella input versions
  • Reading
  • Writing
    • Write v1 (default)
    • Write pre-v1
  • Upgrading legacy files to v1
  • Full worked example
• Using synthetic diagnostic
  • 1.
  • 2.
  • 3.
  • 4.
  • 5.
  • 6.

Todo

Write all of these

• Read kinetics/equilibrium data from A and make input file for gk code B…

• Look at linear/nonlinear outputs…

• Run a scan in parameter A, B, C…

• Generation of input files from data sources like GEQDSK and TRANSP…

• Conversion of input files from one GK code to another…

• Cross-code validation for simple and complicated geometries…

• Performing scans using the code…

• Reading and plotting of basic output data…

• More advanced output analysis (Poincare plots, field line tearing, non-zonal transitions)…

• Applications of generation database for ML training…

• Synthetic diagnostic comparisons…

• Using GK outputs with QL saturation rules…

• Submitting simulations to databases (simDB, GKDB) via IMAS DD…

• Submitting jobs to cluster…

• Storing metadata of simulations…

• Access metric elements (jacobian, gxx, gxy, etc…)…

• How to use synthetic diagnostics…