Observations¶

The [observe] section configures synthetic observation generation. PROTEUS can compute transit and eclipse depth spectra from the simulated atmospheric state using the petitRADTRANS forward model.

The [accretion] section is reserved for late accretion modelling (not yet implemented).

Synthetic observations `[observe]`¶

Parameter	Type	Default	Description
`module`	str or none	`none`	Module to use for calculating synthetic spectra. Choices: `none`, `"petitRADTRANS"`.
`clip_vmr`	float	`1e-08`	Minimum VMR to include a species in radiative transfer. Must be > 0 and < 1.
`reference_pressure`	float	`10`	Reference pressure for synthetic spectrum generation [bar]. Must be > 0.
`source`	str	`"all"`	Composition source selection: 'all', 'outgas', 'profile', or 'offchem'. Choices: `"all"`, `"outgas"`, `"profile"`, `"offchem"`.
`spectrum_type`	str	`"both"`	Synthetic spectrum products to compute: 'both', 'transit', or 'eclipse'. Choices: `"both"`, `"transit"`, `"eclipse"`.
`remove_one_gas`	bool	`true`	If True, generate additional leave-one-out spectra with each gas removed.

petitRADTRANS `[observe.petitRADTRANS]`¶

petitRADTRANS computes wavelength-dependent transit and emission depths from the atmospheric composition and temperature-pressure profile. Its opacity tables are read from $FWL_DATA/prt/input_data (set via the FWL_DATA environment variable at PROTEUS startup).

Composition sources¶

The atmospheric composition passed to petitRADTRANS is controlled by observe.source:

all (default): compute spectra for all available sources
outgas, profile, or offchem: compute spectra only for the selected source

Available source modes:

Source	Description
`outgas`	Constant VMR with height from the outgassing module (helpfile `*_vmr` columns)
`profile`	Full vertical VMR profile from the climate module NetCDF output (`*_vmr` arrays)
`offchem`	Photochemical composition from the VULCAN offline chemistry output

When observe.source = "all", unavailable sources are skipped automatically: profile is skipped when atmos_clim.module = "dummy", and offchem is skipped when atmos_chem.module is none.

When observe.source is set explicitly to profile or offchem, PROTEUS raises an error if the required upstream module is unavailable.

The spectrum product set is controlled by observe.spectrum_type:

both (default): compute both transit and eclipse spectra
transit: compute only transit spectra
eclipse: compute only eclipse spectra

Supported line species¶

The following gases are searched for in the petitRADTRANS correlated-k opacity table directory. A species is included only when its corresponding opacity directory exists under input_data/opacities/lines/correlated_k/:

H2O, H2, CO2, CO, CH4, SO2, H2S, O2, N2, NH3, OH

The species whose opacity file has the broadest wavelength coverage is moved to the front of the line-species list before calling petitRADTRANS. This helps avoid opacity-table overlap issues in the forward-model initialisation.

Rayleigh and CIA species¶

Rayleigh scattering and collision-induced absorption (CIA) species are taken from the constants defined in proteus.utils.constants (prt_rayleigh_species, prt_cia_species) and are filtered to those present in the actual gas mixture.

Profile interpolation¶

Before calling petitRADTRANS, the temperature and VMR profiles are interpolated onto a uniform 100-point log-spaced pressure grid using PCHIP splines. Temperature values are clipped to the range [100.5 K, 3999.5 K] to stay within petitRADTRANS table bounds. If the atmosphere profile is stored with decreasing pressure (surface first), it is reversed to ascending order before interpolation.

Leave-one-out species spectra¶

After computing the baseline spectrum (all species present), PROTEUS can optionally re-run petitRADTRANS once per line species, removing one species at a time. This produces additional spectrum columns in the output CSV that show the contribution of each individual gas to the total signal.

This behaviour is controlled by observe.remove_one_gas. Set it to false to write baseline-only spectra.

Set observe.petitRADTRANS.silent = true to silence the opacity-loading console messages emitted by petitRADTRANS when creating Radtrans objects.

See Output format for the CSV column layout.

Configuration options¶

Parameter	Type	Default	Description
`line_opacity_mode`	str	`"c-k"`	Opacity treatment: 'c-k' (correlated-k) or 'lbl' (line-by-line). Choices: `"c-k"`, `"lbl"`.
`include_rayleigh`	bool	`true`	Include Rayleigh scattering contributions.
`include_cia`	bool	`true`	Include collision-induced absorption contributions.
`silent`	bool	`true`	Suppress petitRADTRANS stdout/stderr during Radtrans initialization.

Late accretion `[accretion]`¶

Parameter	Type	Default	Description
`module`	str or none	`none`	Accretion module to use. Currently only None is supported. Choices: `none`.

Constraints¶

Cross-field constraints enforced when the config file loads:

Synthetic observations require a spatially resolved atmosphere (not dummy).

See also: Model description | Output format | Postprocessing