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GITRm basic workflow

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LC-GA edited this page Jan 19, 2025 · 11 revisions

Required Input Files for GITRm

GITRm requires a series of input files to run simulations effectively. Below is a detailed list of these files:

  1. GITRm Executable
    The main executable file for running simulations.

  2. Mesh File

    • Format: .osh (OmegaH)
    • Represents the computational domain for the simulation.

  3. Partition File

    • Format: .nc (NetCDF4 or classic NetCDF formats)
    • Divides the mesh into smaller domains and assigns each partition to a different GPU.

  4. Background Plasma Profiles

    • Format: .nc
    • Contains essential plasma parameters such as density, temperature, and gradients.

  5. Magnetic Field File

    • Format: .nc
    • Purpose: Derived from magnetic equilibrium reconstructions and used to simulate the plasma background.

  6. Sputtered Flux Profile

    • Format: .nc
    • Purpose: Specifies spatial sampling distribution for the transported species at the start of the simulation.

  7. LU File

    • Format: .nc
    • Purpose: Maps plasma background data to the OmegaH mesh of GITRm.
    • Note: This file must be regenerated if the geometry or plasma background changes (script available in pyGITRm).

  8. ADAS Rates Files

    • Format: One .nc file per species
    • Includes ionization and recombination rates for each simulated particle.

  9. Surface Model File(s)

    • Format: .nc
    • Contains models for sputtered species and material mixing.
    • Note: Multiple files can be used if required. You can choose the model file in the InputConfig file (read below)

  10. Particle Initializer File (Optional)

    • Defines initial particle velocities, positions, and attributes.
    • Note: Usually inferred from other files and not commonly used, but available as an option.

ATTENTION: The format of your input NetCDF (.nc) files depends on how GITRm was built. They must be either in the classic NetCDF format or the HDF5/NetCDF4 format. For more details, refer to the Install GITRm on Omega page.

Since both classic NetCDF and NetCDF4 formats use the same .nc file extension, you will need to manually verify the file format. To check the format, run the following commands:

a) Check for classic NetCDF:

ncdump -k input_file.nc

b) Conversion to NetCDF4 from classic:

nccopy -k netCDF-4 input_file.nc output_file.nc

Input Configuration Files

Once the required input files are ready, two additional files are used to configure and execute the simulation:

  1. inputconfig File

    • Sets input options, including:
      • Number of particles
      • Species
      • Sheath model
      • Sputtered distribution
      • Other parameters
      • ...

  2. run.sh File

    • Contains run commands and a li

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