GUIBRUSHR.Retrieval.ModelCalculation.Classes.Atmosphere module

Atmosphere module for atmospheric modeling and radiative transfer calculations.

This module provides the Atmosphere class for handling atmospheric models, including support for both petitRADTRANS and PyratBay radiative transfer codes.

GUIBRUSHR.Retrieval.ModelCalculation.Classes.Atmosphere.cloud_opas(lambda0_micron, kappa_cond, kappa_opac, omega, xi, temperatures)[source]

Create a cloud opacity function for atmospheric modeling.

This function returns a closure that calculates cloud opacities based on wavelength-dependent scattering and absorption properties.

Parameters:

  • lambda0_micron (float) – Central wavelength in microns

  • kappa_cond (float) – Condensation opacity coefficient

  • kappa_opac (float or None) – Opacity coefficient (if None, calculated from kappa_cond)

  • omega (float) – Width parameter for wavelength dependence

  • xi (float) – Asymmetry parameter

  • temperatures (array_like) – Temperature profile

Returns:

Opacity function that takes wavelengths and pressures as input

Return type:

function

class GUIBRUSHR.Retrieval.ModelCalculation.Classes.Atmosphere.Atmosphere[source]

Bases: object

Atmospheric model class for radiative transfer calculations.

This class handles atmospheric modeling using either petitRADTRANS or PyratBay radiative transfer codes. It manages pressure profiles, chemical compositions, wavelength grids, and stellar spectra for both high and low resolution calculations.

__init__()[source]

Initialize the Atmosphere object with default None values.

update_params(line_species, line_species_isotope, line_species_complete_name_hr, line_species_complete_name_lr, list_condensed_molecules, rayleigh_species, range_min_pressures, range_max_pressures, layers, lbl_high_res, lbl_low_res, resolution=None, instruments_HR=None, instruments_LR=None, continum_opacity=None, mass_vector=None, target=None, chemistry=None, manual_model_obj=None, temp_min=300, temp_max=3000, temp_step=150, initial_params=None, path_default='', rad_mode='Transmission', manual_model_composition=None, retrieval_model='petitRADTRANS', rv_sampling=0.1, additional_opac=False, start_molecs=0)[source]

Update atmospheric model parameters.

This method configures the atmospheric model with species, pressure grid, resolution settings, and other parameters needed for radiative transfer calculations.

Parameters:

  • line_species (list) – List of line species for opacity calculations

  • line_species_isotope (list) – List of isotope-specific line species

  • line_species_complete_name_hr (list) – Complete names of line species HR

  • line_species_complete_name_lr (list) – Complete names of line species LR

  • list_condensed_molecules (list) – List of condensed/cloud species

  • rayleigh_species (list) – List of Rayleigh scattering species

  • range_min_pressures (float) – Minimum pressure in the atmospheric grid

  • range_max_pressures (float) – Maximum pressure in the atmospheric grid

  • layers (int) – Number of atmospheric layers

  • lbl_high_res (float) – Line-by-line high resolution sampling

  • lbl_low_res (float) – Line-by-line low resolution sampling

  • resolution (float, optional) – Spectral resolution

  • instruments_HR (list, optional) – High resolution instruments

  • instruments_LR (list, optional) – Low resolution instruments

  • continum_opacity (list, optional) – Continuum opacity contributors

  • mass_vector (array_like, optional) – Mass fractions for chemical species

  • target (object, optional) – Target object containing system parameters

  • chemistry (str, optional) – Chemistry model type

  • manual_model_obj (object, optional) – Manual model configuration object

  • temp_min (float, default=300) – Minimum temperature for calculations

  • temp_max (float, default=3000) – Maximum temperature for calculations

  • temp_step (float, default=150) – Temperature step for calculations

  • initial_params (dict, optional) – Initial parameter values

  • path_default (str, default="") – Default path for data files

  • rad_mode (str, default="Transmission") – Radiative transfer mode

  • manual_model_composition (dict, optional) – Manual composition specification

  • retrieval_model (str, default="petitRADTRANS") – Radiative transfer code to use

  • rv_sampling (float, default=0.1) – Radial velocity sampling

  • additional_opac (bool, default=False) – Whether to include additional opacity sources

  • start_molecs (int, default=0) – Starting molecule index

set_wl_range(minwlen_lr=None, maxwlen_lr=None, minwlen_hr=None, maxwlen_hr=None)[source]

Set wavelength ranges for high and low resolution calculations.

This method determines the wavelength boundaries for both high and low resolution calculations based on instrument specifications and data ranges. If no explicit ranges are provided, they are automatically determined from the instrument configurations.

Parameters:

  • minwlen_lr (float, optional) – Minimum wavelength for low resolution calculations (microns)

  • maxwlen_lr (float, optional) – Maximum wavelength for low resolution calculations (microns)

  • minwlen_hr (float, optional) – Minimum wavelength for high resolution calculations (microns)

  • maxwlen_hr (float, optional) – Maximum wavelength for high resolution calculations (microns)

init_pyratbay(output_folder, initial_params)[source]

Initialize PyratBay radiative transfer module.

This method sets up the PyratBay atmospheric model with the specified configuration and identifies available opacity models for clouds and Rayleigh scattering.

Parameters:

  • output_folder (str or Path) – Directory for PyratBay output files

  • initial_params (dict or None) – Initial parameter values for the model

read_opacities(table_output_file=None, path_target='', stellar_spectrum_type_lr='Phoenix', stellar_spectrum_type_hr='Phoenix', min_hwhm_hr=1.5, instrument_LR=None, stellar_spectrum_type_lr_mode='Point by Point', use_hr_linelists_for_lr=False)[source]

Initialize opacity tables and stellar spectra for radiative transfer.

This method orchestrates the setup of petitRADTRANS Radtrans objects for both high and low resolution calculations. It delegates to specialized methods for LR and HR initialization, loads opacity data, and prepares stellar spectra for emission calculations.

The method handles three resolution scenarios: 1. Low resolution only: Uses correlated-k opacity tables 2. High resolution only: Uses line-by-line opacity mode 3. Mixed mode: HR linelists binned to LR resolution (use_hr_linelists_for_lr)

Parameters:

  • table_output_file (str, optional) – Path to output file for error messages

  • path_target (str, default="") – Path to target-specific data directory

  • stellar_spectrum_type_lr (str, default="Phoenix") – Type of stellar spectrum for LR (“Planck”, “Phoenix”, or “Integral”)

  • stellar_spectrum_type_hr (str, default="Phoenix") – Type of stellar spectrum for HR (“Planck” or path to spectrum file)

  • min_hwhm_hr (float, default=1.5) – Minimum pixel velocity width for high resolution (km/s)

  • instrument_LR (list, optional) – List of instruments for low resolution calculations

  • stellar_spectrum_type_lr_mode (str, default="Point by Point") – Type of stellar spectrum for LR (“Point by Point” or “Integral”)

  • use_hr_linelists_for_lr (bool, default=False) – Use high resolution line lists for low resolution calculations

Warning

If opacity initialization fails, the error is caught internally, a diagnostic message is written to table_output_file (if provided), and the process exits via exit(). No exception is raised to the caller.

Notes

  • Stellar spectra only loaded for emission mode (not transmission)

  • Sets attributes: atmosphere_lr, atmosphere_hr, stellar_spectrum (dict with “model_PRT_LR” and “model_PRT_HR” keys), wl_lr_nm, wl_hr_nm

calc_model(temperature, mass_fraction, vmr, MMW, dict_calc_model, HR=True)[source]

Compute the transmission or emission spectrum for given atmospheric model.

This method calculates either transmission or emission spectra using either petitRADTRANS or PyratBay radiative transfer codes, depending on the configuration.

Parameters:

  • temperature (array_like) – Temperature profile

  • mass_fraction (dict) – Mass fractions of atmospheric species

  • vmr (dict) – Volume mixing ratios of atmospheric species

  • MMW (array_like) – Mean molecular weight profile

  • dict_calc_model (dict) – Dictionary containing model parameters

  • HR (bool, default=True) – Whether to use high resolution calculation

Returns:

  • wl_full_resolution (array_like) – Wavelengths (nm)

  • model (array_like or None) – Raw model output (transit radii or flux). None when using PyratBay.

  • depth_full_resolution (array_like) – Final spectrum (transmission depth or emission)

calc_model_contribution(temperature, mass_fraction, MMW, dict_calc_model, HR=True)[source]

Calculate transmission contribution function for atmospheric layers.

This method computes the contribution of different atmospheric layers to the total transmission spectrum, useful for understanding which pressure levels dominate the observed signal.

Parameters:

  • temperature (array_like) – Temperature profile

  • mass_fraction (dict) – Mass fractions of atmospheric species

  • MMW (array_like) – Mean molecular weight profile

  • dict_calc_model (dict) – Dictionary containing model parameters

  • HR (bool, default=True) – Whether to use high resolution calculation

Returns:

  • wl (array_like) – Wavelengths (nm)

  • contribution (array_like) – Transmission contribution function

opacity_contribution(temperatures, mass_fractions, MMW, dict_calc_model, HR=True)[source]

Generate opacity contribution plots for atmospheric species.

This method creates plots showing the relative contribution of different opacity sources (molecular species, clouds, hazes) to the total spectrum.

Parameters:

  • temperatures (array_like) – Temperature profile

  • mass_fractions (dict) – Mass fractions of atmospheric species

  • MMW (array_like) – Mean molecular weight profile

  • dict_calc_model (dict) – Dictionary containing model parameters

  • HR (bool, default=True) – Whether to use high resolution calculation

Returns:

opacity_contributions – Figure object with opacity contribution plots, or None if failed

Return type:

matplotlib.figure.Figure or None