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. Atmospheric chemistry can also be coupled live during a run. This page covers all three workflows.

Atmospheric chemistry with VULCAN

PROTEUS can couple to the VULCAN chemical kinetics model to compute atmospheric composition. The atmos_chem.when configuration variable controls when chemistry is calculated. There are three modes:

Mode	`atmos_chem.when`	Description
Manually	`"manually"`	Chemistry is skipped during simulation. Run it yourself afterwards via the CLI.
Offline	`"offline"`	Chemistry runs once automatically after the simulation finishes, on the final atmospheric state.
Online	`"online"`	Chemistry runs at every output snapshot during the simulation, coupled to the evolving atmosphere.

All three modes require atmos_chem.module = "vulcan" and the AGNI atmosphere module (atmos_clim.module = "agni").

Manually mode (default)

When atmos_chem.when = "manually" (the default), no chemistry is calculated during or after the simulation. You can run it yourself at any time using the CLI:

proteus offchem -c [cfgfile]

This is useful when you want to experiment with different chemistry settings (for example network or photochemistry) without re-running the full simulation.

Offline mode

When atmos_chem.when = "offline", PROTEUS automatically runs VULCAN once after the main simulation loop completes. It uses the final atmospheric temperature-pressure profile and composition as input. Results are written to offchem/vulcan.csv in the output directory.

This is the recommended mode for most use cases: it adds chemistry as a post-processing step with minimal overhead.

Online mode

When atmos_chem.when = "online", PROTEUS runs VULCAN at every output snapshot (controlled by params.out.write_mod) during the main simulation loop. This couples the chemistry to the evolving thermal state of the atmosphere.

Key differences from offline mode:

Per-snapshot output: Each snapshot produces its own output file (vulcan_{year}.csv) rather than a single vulcan.csv.
One-time network compilation: The chemical reaction network is compiled only once on the first snapshot, then reused for subsequent snapshots.
Skipped when desiccated: If the planet loses its entire volatile inventory, online chemistry is skipped for subsequent snapshots.

Online mode is more expensive but captures the time evolution of atmospheric chemistry alongside the thermal evolution.

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 results can be postprocessed to generate synthetic observations. Transmission and emission spectra are produced from the modelled temperature-pressure profile and atmospheric composition. The composition can be set by the output of the offline chemistry calculation (see the configuration file).

Access the synthetic-observation functionality via the CLI:

proteus observe -c [cfgfile]

PROTEUS will perform this step automatically if it is enabled in the configuration file. See the observations reference for the 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.