Output format¶

PROTEUS writes simulation output to a directory inside output/. This page documents the structure of that directory and the contents of the main output files.

Directory structure¶

A completed PROTEUS run produces:

output/<run_name>/
    runtime_helpfile.csv    # Main time-series output (tab-separated)
    init_coupler.toml       # Copy of the configuration used
    status                  # Exit status code and description
    proteus_00.log          # Log file (subsequent resumes: proteus_01.log, ...)
    plots/                  # Generated diagnostic plots
        plot_global.png
        plot_escape.png
        plot_interior.png
        ...
    data/                   # Module-specific output files
        <iter>_atm.nc       # Atmosphere profiles (NetCDF, per snapshot)
        <iter>_int.nc       # Interior profiles (NetCDF, per snapshot)
        zalmoxis_output.dat # Zalmoxis structure profile (latest)
        spider_eos/         # Cached EOS lookup tables (if Aragog/SPIDER)
        ...
    observe/                # Synthetic observations (if enabled)
        transit_<source>_synthesis.csv   # Transit depth spectra
        eclipse_<source>_synthesis.csv   # Eclipse depth spectra

<source> is outgas, profile, or offchem, depending on observe.source. With observe.source = "all" (default), PROTEUS writes one pair of files per available source.

Status codes¶

The status file contains a single integer followed by a human-readable description. The codes are:

Helpfile columns¶

The runtime_helpfile.csv is a tab-separated file with one row per coupling iteration. All quantities use SI units unless noted otherwise. The columns are grouped by category below.

Time¶

Orbital parameters¶

Satellite (if enabled)¶

Planet structure¶

Temperatures¶

Energy fluxes¶

Interior state¶

Stellar properties¶

Atmospheric composition¶

For each gas species (H2O, CO2, N2, H2, CH4, CO, SO2, H2S, NH3, S2):

Elemental budgets¶

For each element (H, C, N, O, S):

Bulk atmosphere¶

Redox state¶

Escape¶

Observables¶

Solvus and miscibility (when global_miscibility is enabled)¶

Synthetic observation CSV columns¶

Files in observe/ are tab-separated. They always contain:

• Wavelength/um
• None/ppm (baseline spectrum with all included gases)

When observe.remove_one_gas = true, additional columns are included:

• <SPECIES>_removed/ppm for each leave-one-out run

Accretion mode columns (when temperature_mode = 'accretion')¶

Energy conservation diagnostics (Aragog only)¶

Synthetic observation output files¶

When observe.module = "petitRADTRANS", PROTEUS writes CSV files to observe/ for each composition source (outgas, profile, offchem). Files are named transit_<source>_synthesis.csv and eclipse_<source>_synthesis.csv.

The set of files is controlled by observe.spectrum_type:

• both: writes both transit and eclipse files
• transit: writes transit files only
• eclipse: writes eclipse files only

All CSV files are tab-separated with a one-line header. The first column is always the wavelength grid; subsequent columns are depth values in ppm:

The number of *_removed columns varies depending on which species have opacity tables present in $FWL_DATA/prt/input_data and exceed the clip_vmr threshold at the time of the calculation.

The plot_spectra diagnostic overlays all columns on a two-panel figure: the upper panel shows transit depths, the lower shows eclipse depths. The baseline (None/ppm) is drawn in black; each removed-species line is coloured by species identity.

Diagnostic plots¶

PROTEUS generates diagnostic plots at intervals controlled by params.out.plot_mod. Available plot types: