Atmosphere and chemistry

The [atmos_clim] section configures the atmospheric climate module (radiative-convective structure and surface energy balance). The [atmos_chem] section configures atmospheric chemistry (photochemical kinetics).

Submodule documentation: AGNI | SOCRATES | JANUS | VULCAN. See also Model description.

Atmosphere climate `[atmos_clim]`

Parameter	Type	Default	Description
`module`	str	`"agni"`	Climate module: `agni` (radiative-convective atmosphere model), `janus` (prescribed pseudoadiabatic model), `dummy` (parameterised)
`spectral_group`	str	`"Honeyside"`	Opacity k-table set (shared by AGNI and JANUS; see options here)
`spectral_bands`	str	`"48"`	Number of wavenumber bands in k-tables
`num_levels`	int	`50`	Number of vertical atmosphere levels (minimum 15)
`p_top`	float	`1e-6`	Top-of-atmosphere pressure [bar]
`p_obs`	float	`0.02`	Observation pressure level [bar] (defines transit radius)
`overlap_method`	str	`"ee"`	Gas overlap method: `ro`, `rorr`, `ee` (equivalent extinction)

Radiative properties

Parameter	Type	Default	Description
`rayleigh`	bool	`true`	Enable Rayleigh scattering
`cloud_enabled`	bool	`false`	Enable water cloud radiative effects
`cloud_alpha`	float	`0.0`	Condensate retention fraction [0, 1]
`aerosols_enabled`	bool	`false`	Enable aerosol radiative effects (AGNI only)
`albedo_pl`	float or str	`0.0`	Planetary bond albedo: a constant float, or a path to a CSV lookup table
`surf_greyalbedo`	float	`0.1`	Grey surface albedo (used when `agni.surf_material = "greybody"`)

Surface boundary condition

Parameter	Type	Default	Description
`surf_state`	str	`"skin"`	Energy balance scheme: `mixed_layer` (ocean-like), `fixed` (lock to magma temperature), `skin` (conductive skin layer)
`surface_d`	float	`0.01`	Conductive skin thickness [m]
`surface_k`	float	`2.0`	Conductive skin conductivity [W m\(^{-1}\) K\(^{-1}\)]

Solver limits

Parameter	Type	Default	Description
`tmp_minimum`	float	`0.5`	Temperature floor [K]

AGNI `[atmos_clim.agni]`

AGNI is a detailed radiative-convective equilibrium solver written in Julia. It iteratively solves for the atmospheric temperature-pressure profile that balances absorbed stellar radiation with outgoing thermal emission and interior heat flux.

Physics

Parameter	Type	Default	Description
`solve_energy`	bool	`true`	Iterative energy-conserving T(p) profile
`convection`	bool	`true`	Include mixing-length convective energy fluxes
`conduction`	bool	`true`	Conductive heat transport (Fourier)
`sens_heat`	bool	`true`	Sensible heat flux at surface
`rainout`	bool	`true`	Volatile condensation and evaporation
`oceans`	bool	`true`	Surface liquid water oceans
`latent_heat`	bool	`false`	Latent heat from condensation/evaporation
`real_gas`	bool	`false`	Real-gas EOS where available
`chemistry`	str or none	`"none"`	Atmospheric chemistry: `none` or `eq` (FastChem equilibrium)
`mlt_criterion`	str	`"s"`	Convection criterion: `s` (Schwarzschild) or `l` (Ledoux)

Surface properties

Parameter	Type	Default	Description
`surf_material`	str	`"greybody"`	Surface scattering model; `"greybody"` uses `surf_greyalbedo`
`surf_roughness`	float	`1e-3`	Surface roughness scale [m]
`surf_windspeed`	float	`2.0`	Characteristic wind speed [m s\(^{-1}\)]

Condensation

Parameter	Type	Default	Description
`phs_timescale`	float	`1e6`	Phase change relaxation timescale [s]
`evap_efficiency`	float	`0.01`	Raindrop re-evaporation efficiency [0, 1]

Solver tuning

Parameter	Type	Default	Description
`solution_atol`	float	`0.5`	Newton solver absolute tolerance [W m\(^{-2}\)]
`solution_rtol`	float	`0.15`	Newton solver relative tolerance
`psurf_thresh`	float	`0.1`	Switch to transparent atmosphere-free solver when surface pressure is less than this [bar]
`dx_max`	float	`35.0`	Maximum Newton step per iteration [K]
`dx_max_ini`	float	`50.0`	Maximum Newton step during first few PROTEUS loops [K]
`max_steps`	int	`200`	Maximum Newton iterations per call
`perturb_all`	bool	`false`	Recompute full Jacobian each iteration
`ini_profile`	str	`"isothermal"`	Initial T(p) guess: `isothermal`, `loglinear`, `dry_adiabat`, `analytic`
`ls_default`	int	`2`	Linesearch method: 0 (none), 1 (golden section), 2 (backtracking)
`fdo`	int	`2`	Finite-difference order for the numerical Jacobian: `2` or `4`
`verbosity`	int	`1`	AGNI log level: 0 (silent), 1 (info), 2 (debug)

Spectral and gas allocation

Parameter	Type	Default	Description
`spectral_file`	str or none	`none`	Path to an AGNI spectral file, or `"greygas"` for the grey-gas scheme; `none` uses `spectral_group`/`spectral_bands`
`grey_opacity_lw`	float	`10`	Grey longwave opacity [m\(^2\) kg\(^{-1}\)], used when `spectral_file = "greygas"`
`grey_opacity_sw`	float	`1e-4`	Grey shortwave opacity [m\(^2\) kg\(^{-1}\)], used when `spectral_file = "greygas"`
`check_safe_gas`	bool	`true`	Require at least one "safe" gas (dry, with opacity and thermodynamic data) when allocating the atmosphere

FastChem equilibrium chemistry (used when chemistry = "eq")

Parameter	Type	Default	Description
`fastchem_floor`	float	`1000.0`	Minimum temperature sent to FastChem [K]
`fastchem_maxiter_chem`	int	`60000`	Maximum FastChem iterations (chemistry)
`fastchem_maxiter_solv`	int	`20000`	Maximum FastChem iterations (internal solver)
`fastchem_xtol_chem`	float	`1e-4`	FastChem convergence tolerance (chemistry)
`fastchem_xtol_elem`	float	`1e-4`	FastChem convergence tolerance (elemental)

JANUS `[atmos_clim.janus]`

JANUS is a fast 1-D radiative-convective atmosphere model. It is computationally lighter than AGNI and suitable for parameter sweeps.

Parameter	Type	Default	Description
`F_atm_bc`	int	`0`	Outgoing flux boundary: 0 (top of atmosphere) or 1 (surface)
`tropopause`	str or none	`"none"`	Tropopause scheme: `none`, `skin`, `dynamic`
`cloud_alpha`	float	`0.0`	Condensate retention fraction [0, 1]
`tmp_maximum`	float	`5000.0`	Solver temperature ceiling [K]

Dummy atmosphere `[atmos_clim.dummy]`

A grey-body parameterisation: \(T_\mathrm{rad} = T_\mathrm{surf} \cdot (1 - \gamma)\).

Parameter	Type	Default	Description
`gamma`	float	`0.5`	Atmosphere opacity factor; 0 = transparent, 1 = zero OLR
`height_factor`	float	`3.0`	Observable height as multiple of scale height
`fixed_flux`	float	`-1.0`	If > 0, return this constant \(F_\mathrm{atm}\) [W m\(^{-2}\)]

Atmospheric chemistry `[atmos_chem]`

Parameter	Type	Default	Description
`module`	str or none	`"none"`	Chemistry module: `none` (skip), `vulcan` (photochemistry), `dummy`
`when`	str	`"manually"`	When to run: `manually` (user-triggered), `offline` (at simulation end), `online` (each snapshot)
`photo_on`	bool	`true`	Enable photochemistry
`Kzz_on`	bool	`true`	Enable eddy diffusion
`Kzz_const`	float or none	`none`	Constant \(K_{zz}\) [cm\(^2\) s\(^{-1}\)]; `none` = computed profile
`moldiff_on`	bool	`true`	Enable molecular diffusion
`updraft_const`	float	`0.0`	Constant updraft velocity [cm s\(^{-1}\)]

VULCAN `[atmos_chem.vulcan]`

VULCAN solves photochemical kinetics for atmospheric composition, computing steady-state mixing ratios from a chemical reaction network.

Parameter	Type	Default	Description
`network`	str	`"SNCHO"`	Chemical network: `CHO`, `NCHO`, `SNCHO`
`ini_mix`	str	`"profile"`	Initial mixing ratios: `profile` (from atmosphere module) or `outgas` (from outgassing)
`fix_surf`	bool	`false`	Hold surface mixing ratios fixed
`make_funs`	bool	`true`	Generate reaction network functions
`yconv_cri`	float	`0.05`	Convergence criterion (mixing ratio change)
`slope_cri`	float	`0.0001`	Convergence criterion (rate of change)
`clip_fl`	float	`1e-20`	Stellar flux floor [erg s\(^{-1}\) cm\(^{-2}\) nm\(^{-1}\)]
`clip_vmr`	float	`1e-10`	Neglect species below this VMR
`save_frames`	bool	`false`	Save plot frames during iterations

Atmosphere and chemistry

Atmosphere climate [atmos_clim]

AGNI [atmos_clim.agni]

JANUS [atmos_clim.janus]

Dummy atmosphere [atmos_clim.dummy]

Atmospheric chemistry [atmos_chem]

VULCAN [atmos_chem.vulcan]