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Data Output & Restart Files

GeoDynamo.jl writes diagnostics, checkpoints, and restart files through the NetCDF-based outputs_writer.jl. The system is designed to scale with MPI: each rank writes only the data it owns, avoiding collective I/O bottlenecks.

OutputConfig

The OutputConfig struct controls how data is written to NetCDF files. Create instances using:

  • default_config() - Creates default configuration
  • output_config_from_parameters() - Seeds from current GeoDynamoParameters
  • with_output_precision(config, T) - Changes precision to type T
  • with_independent_writes(config, flag) - Enables/disables independent writes

Key flags:

  • output_precision – choose Float32 to reduce file size; metadata and diagnostics stay in Float64.
  • independent_writes – when true (default), every rank writes geodynamo_output_rank_XXXX_time_T.nc. Disable to enforce MPI.Barrier synchronisation at the cost of scalability.
  • output_dir / filename_prefix – location and prefix for both output and restart files.
  • compression_level – NetCDF deflate level (0 disables compression).

Use output_config_from_parameters() to seed an OutputConfig from the current GeoDynamoParameters, then tweak it with with_output_precision or with_independent_writes.

File Layout

Each NetCDF file stores:

  • Coordinates: theta, phi, r, along with spherical-harmonic index arrays (l_values, m_values).
  • Spectral fields: real/imaginary pairs for velocity (toroidal/poloidal), magnetic field, temperature, composition.
  • Physical fields: optional temperature/composition grids when output_space includes physical data.
  • Diagnostics: scalar variables summarising energy, RMS, spectral peaks, etc.
  • Metadata: geometry, MPI rank, wall-clock time, simulation step.

Per-rank files make post-processing easy—filter by rank_0003 to grab data from a specific MPI rank.

NetCDF Boundaries

Boundary conditions can also be sourced from NetCDF. The helper config/netcdf_boundaries.jl and the Boundary Conditions module understand files containing:

  • boundary_type (Dirichlet, Neumann, etc.)
  • inner_values / outer_values
  • Time-dependent series with interpolation metadata

Refer to docs/src/NETCDF_BOUNDARIES.jl (legacy) or the developer guide for template creation.

Restart Files

write_restart! mirrors the output structure and adds restart-specific scalars (last_output_time, output_count, restart_count). Use read_restart! to populate a fresh SimulationState and TimeTracker:

restart_data, metadata = read_restart!(tracker, "output", 1.0, config)

Tips

  • Keep restart cadence (restart_interval) longer than output cadence unless you need frequent checkpoints.
  • To resume with new precision, load the restart and apply with_output_precision before continuing.
  • MPI ranks search for files matching their rank_XXXX suffix; avoid manual renames.

Diagnostics & Conversion

The extras/spectral_to_physical.jl script converts spectral NetCDF files to physical grids in batch mode. Run it with:

julia --project extras/spectral_to_physical.jl --input output --output physical

The script honours the same precision flags and uses the stored SHTnsKit configuration to perform inverse transforms.