Postprocessing and chemistry¶

After a PROTEUS simulation has run, its atmospheric state can be postprocessed to compute detailed chemistry, synthetic observations, and multi-angle thermal profiles. This page covers all three workflows.

Atmospheric chemistry with VULCAN¶

PROTEUS can run the VULCAN chemical kinetics model on the atmospheric state it has simulated. VULCAN needs atmos_chem.module = "vulcan" and the AGNI atmosphere (atmos_clim.module = "agni"). atmos_chem.module = "dummy" writes parameterised profiles in the same format without a kinetics solver, for testing.

When chemistry runs: atmos_chem.mode¶

proteus offchem runs the chemistry whatever the mode, so a finished run can be postprocessed with other chemistry settings (for example another network, or photochemistry off) without running the evolution again:

proteus offchem -c [cfgfile]

Which snapshots: atmos_chem.times¶

The snapshots run in order of increasing time.

Initial composition: atmos_chem.vulcan.ini_mix¶

VULCAN integrates from an initial composition to a steady state, and the initial composition changes how many steps it needs to converge.

"previous" is meant for times = "all" or a list, where consecutive snapshots are close in time and in composition, to help convergence.

Output files¶

Snapshot times in file names use the sub-year form of the other snapshots: 12p320 for t = 12.32 yr.

Each chemistry call first clears offchem/ (and its VULCAN input files), while the data/*_chem.nc files are kept. The chemistry plot (plots/plot_chem_atmosphere.*) shows the latest chemistry snapshot.

Examples¶

Run VULCAN once on the final state, automatically at the end of the simulation:

[atmos_chem]
    module = "vulcan"
    mode   = "offline"
    times  = "end"

Postprocess every snapshot, each run starting from the result of the one before:

[atmos_chem]
    module = "vulcan"
    mode   = "offline"
    times  = "all"

    [atmos_chem.vulcan]
        ini_mix  = "previous"
        fix_surf = true

Run nothing automatically, then postprocess three chosen times with proteus offchem -c [cfgfile]:

[atmos_chem]
    module = "vulcan"
    mode   = "none"
    times  = [1e3, 1e5, 1e7]   # yr

Chemistry configuration¶

The chemistry behaviour is further controlled by settings under [atmos_chem] and [atmos_chem.vulcan] in the configuration file. Key options include:

• atmos_chem.vulcan.network: Chemical network to use ("CHO", "NCHO", or "SNCHO")
• atmos_chem.photo_on: Enable photochemistry
• atmos_chem.Kzz_on: Enable eddy diffusion mixing

See the atmosphere and chemistry reference for the full list of options.

Synthetic observations¶

PROTEUS can generate synthetic transit and eclipse depth spectra from the simulated atmospheric state using petitRADTRANS. Spectra are produced as "perfect" observations — no telescope noise model is applied — so they represent the intrinsic planetary signal.

Access the synthetic-observation functionality via the CLI:

proteus observe -c [cfgfile]

PROTEUS also runs this step automatically at the end of a simulation when observe.module = "petitRADTRANS" is set in the configuration file.

Composition sources¶

Spectra are computed from composition sources controlled by observe.source:

• all (default): run all available sources below
• outgas, profile, or offchem: run only that source

Available sources:

Output files¶

For each source, two CSV files are written to observe/ inside the run directory:

• transit_<source>_synthesis.csv — primary transit depth
• eclipse_<source>_synthesis.csv — secondary eclipse depth

Use observe.spectrum_type to choose which products are written:

• both (default): writes both files above
• transit: writes only transit_<source>_synthesis.csv
• eclipse: writes only eclipse_<source>_synthesis.csv

Both files are tab-separated with the following column layout:

Set observe.remove_one_gas = false to disable the <SPECIES>_removed/ppm columns and write baseline-only spectra.

The baseline column uses the full set of line species found in the petitRADTRANS opacity table directory ($FWL_DATA/prt/input_data). Species below the clip_vmr threshold are excluded.

Plotting¶

The plot_spectra diagnostic produces a two-panel PDF figure:

• Upper panel: primary transit depth as a function of wavelength.
• Lower panel: secondary eclipse depth as a function of wavelength.

Both panels overlay the baseline spectrum (black) with all per-species removed spectra (coloured by species). The figure is saved to plots/plot_spectra_profile.pdf (or .png depending on params.out.plot_fmt).

See the Observations configuration reference for all available options.

Multiprofile analysis with AGNI¶

PROTEUS can postprocess the planet's atmosphere for a number of zenith angles. This yields localised thermal profiles based on the angle of irradiation on the atmosphere, which is particularly useful for tidally locked planets.

Access this functionality via the CLI, from within the PROTEUS directory:

julia tools/multiprofile_postprocess.jl output/[outputdir] 0,36,45,89

This example computes results for four zenith angles (0, 36, 45, 89), but the script works for any number of zenith angles and creates a new ..._atm_z{angle}.nc file in the data/ directory of the output folder for each angle.

See also: Usage overview | Running and output | Atmosphere and chemistry reference | Observations reference | VULCAN submodule