opac.yaml

The preproccessing of exorad using the python package exorad_opac requires a parameter file with the name opac.yaml in the input folder.

The opac.yaml comes with three mandatory sections:

The star section sets the stellar parameters (as needed for the radiative transfer)

The temp_init section which specifies the input temperature profile for MITgcm

The press_init section which sets the vertical pressure grid of MITgcm

(optionally) The grid section which sets properties on the opacity grid

(optionally) The chemistry section which sets properties on the chemistry for the opacities

(optionally) The prt section which sets arguments for petitRADTRANS (when creating the Radtrans object)

Many parameters have defaults that exorad_opac will fallback to if those are not set in opac.yaml. Checkout DEFAULT_<name> values in config.py.

An example opac.yaml file can look like this:

star:   # Section containing the stellar properties of the host star
  Tstar: 4520
  Rstar: 0.667
  semimajoraxis: 0.01526
  flux_scaling: BB

temp_init:   # Section containing the temperature init of MITgcm
  theta_deep: 1400
  warn_theta_inversion: False

press_init:  # Section containing the vertical grid of MITgcm
  np_log: 41
  zero_eps: 2.0e-5
  p0: 700

chemistry:  # Section containing FeH and CO for chemical equilibrium in opacities
  FeH: 0.0
  CO: 0.55
  use_temp_init: True

grid:  # Section containing arguments for the temperature gridding in the opacity grid

prt:  # Section containing arguments of the Radtrans object of petitRADTRANS

expeRT/MITgcm needs to know and set the incident stellar flux. The star section in opac.yaml helps to compute that.

Paramters in `opac.yaml` - `star`
Parameter	Unit	Meaning
`Tstar`	K	Temperature of the host star
`Rstar`	solar radii	radius of the host star
`semimajoraxis`	AU	orbital seperation of planet
`flux_scaling`	str, or erg/cm^2/s/Hz	the scaling of the stellar intensity. Per default it scales to a black body, can be a specific value as well

There is a large variety on possible input parameters for the initial temperature profile. The default temperature profile will equal to the profile used in Schneider et al. (2022) with the minimum parameter to set: theta_deep.

All parameters are passed down to ic.py to the function calc_init_temperature(), where many parameters can be hidden in **kwargs.

Paramters in `opac.yaml` - `temp_init`
Parameter	Unit	Meaning
`theta_deep`	K	Temperature of the initial temperature profile at 1 bar (adiabat correction)
`warn_theta_inversion`	bool	default to `False`. If true, it will fail, when there is an inversion in the temperature profile at depth.
`profile`	string	“guillot”, “parmentier”, “heng” or “isothermal” for guillot2010 or parmentier2015 or heng2011 or isothermal models respectively.
`use_thorngren`	bool	Use or dont use the intirior temperature fit from Thorngren et al. (2018) as a guess for the initial intirior temp.
`T_int`	K	Manually chosen T_int
`p_min_deep`, `p_max_deep`	bar	minimal and maximal pressure between which the adiabat is interpolated to the upper atmosphere temperature
more		see the individual temperature functions (`isothermal`, `heng`, `guillot_global`, `tp_parmentier`) in `ic.py` for more parameters

Opacities are computed by assuming chemical equilibrium applying the equilibrium interpolator of petitRADTRANS. There are two parameters that you can change for that:

Paramters in opac.yaml - chemistry

Parameter

Unit

Meaning

CO

number

C/O ratio (default=0.55 - solar)

FeH

log

log metalicity (default=0.0 - solar)

use_temp_init

bool

Use the initial temperature profile to calculate the MMW and cp

There are also a few parameters that can be tweaked for the temperature gridding in the final opacity grid. These things are set in the grid section of opac.yaml.

Paramters in `opac.yaml` - `grid`
Parameter	Unit	Meaning
`tmin`	K	Minimal temperature of the precalculated opacity grid
`tmax`	K	Maximum temperature of the precalculated opacity grid
`tresolution`	int	Temperatureresolution of the precalculated opacity grid (e.g., how many T-points)
`interpolate_chem`	bool	If the petitRADTRANS poormans interpolation scheme should be used for premixing. Default False, which means that easychem is used (takes a bit longer)

The vertical coordinate in MITgcm can be set via the press_init section. These are the arguments:

Paramters in `opac.yaml` - `press_init`
Parameter	Unit	Meaning
`np_log`	int	Number of logarithmic vertical layers
`zero_eps`	bar	Difference between the upper most pressure point to 0
`p0`	bar	boundary pressure
`dp_lin`	bar	Pressure differences in the linear part of the grid

Warning

Do not forget to match SIZE.h!

exorad_opac uses petitRADTRANS to create opacities. You can initialise exorad_opac in the same way as you would use petitRADTRANS. It is easily possible to specify line species, wlen regions, etc or whatever in the prt section of opac.yaml. Some parameters have default values in exorad_opac. You can easily overwrite these values if you use your own values in opac.yaml.

These are the default values:

prt:
    line_species: ['H2O_Exomol', 'Na_allard', 'K_allard', 'CO2', 'CH4', 'NH3', 'CO_all_iso_Chubb', 'H2S', 'HCN', 'SiO', 'PH3', 'TiO_all_Exomol', 'VO', 'FeH']
    rayleigh_species: ['H2', 'He']
    continuum_opacities: ['H2-H2', 'H2-He', 'H-']
    wlen_bords_micron: [0.2, 100.]
    # + any other argument of the Radtrans class

This is equivilant to

from petitRADTRANS import Radtrans

line_species= ['H2O_Exomol', 'Na_allard', 'K_allard', 'CO2', 'CH4', 'NH3', 'CO_all_iso_Chubb', 'H2S', 'HCN', 'SiO', 'PH3', 'TiO_all_Exomol', 'VO', 'FeH']
rayleigh_species= ['H2', 'He']
continuum_opacities= ['H2-H2', 'H2-He', 'H-']
wlen_bords_micron= [0.2, 100.]

atmosphere = Radtrans(..., line_species=line_species, rayleigh_species=rayleigh_species, continuum_opacities=continuum_opacities, wlen_bords_micron=wlen_bords_micron)