petitRADTRANS.retrieval.models

petitRADTRANS.retrieval.models#

Models Module

This module contains a set of functions that generate the spectra used in the petitRADTRANS retrieval. This includes setting up the pressure-temperature structure, the chemistry, and the radiative transfer to compute the emission or transmission spectrum.

All models must take the same set of inputs:

prt_objectpetitRADTRANS.RadTrans

This is the pRT object that is used to compute the spectrum It must be fully initialized prior to be used in the model function

parametersdict

A dictionary of Parameter objects. The naming of the parameters must be consistent between the Priors and the model function you are using.

PT_plot_modebool

If this argument is True, the model function should return the pressure and temperature arrays before computing the flux.

amrbool

If this parameter is True, your model should allow for reshaping of the pressure and temperature arrays based on the position of the clouds or the location of the photosphere, increasing the resolution where required. For example, using the fixed_length_amr function defined below.

Attributes#

PGLOBAL

Functions#

_compute_gravity(parameters)

emission_model_diseq(prt_object, parameters[, ...])

Disequilibrium Chemistry Emission Model

emission_model_diseq_simple_patchy_clouds(prt_object, ...)

Deprecated, to be removed in future version

emission_model_diseq_patchy_clouds(prt_object, parameters)

Disequilibrium Chemistry Emission Model

guillot_emission(prt_object, parameters[, ...])

Emission spectrum calculation for the Guillot 2010 temperature profile.

guillot_emission_add_gaussian_temperature(prt_object, ...)

Emission spectrum calculation for the Guillot 2010 temperature profile.

guillot_patchy_emission(prt_object, parameters[, ...])

Deprecated, to be removed in future version

interpolated_profile_emission(prt_object, parameters)

This model computes a emission spectrum based a spline temperature-pressure profile.

gradient_profile_emission(prt_object, parameters[, ...])

This model computes a emission spectrum based a gradient temperature-pressure profile (Zhang 2023).

power_law_profile_emission(prt_object, parameters[, ...])

This model computes a emission spectrum based a gradient temperature-pressure profile (Zhang 2023).

guillot_transmission(prt_object, parameters[, ...])

Transmission Model, Guillot Profile

guillot_patchy_transmission(prt_object, parameters[, ...])

Deprecated

madhushudhan_seager_emission(prt_object, parameters[, ...])

Transmission Model, Madhusudhan Seager 2009 Profile

madhushudhan_seager_transmission(prt_object, parameters)

Transmission Model, Madhusudhan Seager 2009 Profile

madhu_seager_patchy_transmission(prt_object, parameters)

Deprecated

isothermal_transmission(prt_object, parameters[, ...])

Equilibrium Chemistry Transmission Model, Isothermal Profile

power_law_profile_transmission(prt_object, parameters)

This model computes a emission spectrum based a gradient temperature-pressure profile (Zhang 2023).

add_blackbody_cpd_model(parameters, wavelengths)

Calculates the flux of a blackbody with area 4*pi*disk_radius^2 and temperature T_disk_blackbody.

initialize_pressure(press, parameters, amr)

Provide the pressure array correctly sized to the prt_object in use, accounting for

set_pglobal(press, parameters)

Check to ensure that the global pressure array has the correct length.

calculate_emission_spectrum(prt_object, parameters, ...)

Calls Radtrans.calculate_flux to compute the emission spectrum of an atmosphere.

calculate_transmission_spectrum(prt_object, ...)

_summary_

pglobal_check(press, shape, scaling)

Check to ensure that the global pressure array has the correct length.

Module Contents#

petitRADTRANS.retrieval.models.PGLOBAL#
petitRADTRANS.retrieval.models._compute_gravity(parameters)#
petitRADTRANS.retrieval.models.emission_model_diseq(prt_object, parameters, pt_plot_mode=False, amr=True)#

Disequilibrium Chemistry Emission Model

This model computes an emission spectrum based on the temperature profile of (Molliere 2020). (Dis)equilibrium or free chemistry, can be used. The use of easychem for on-the-fly (dis)equilibrium chemistry calculations is supported, but is currently under development. Many of the parameters are optional, but must be used in the correct combination with other parameters.

Args:
prt_objectobject

An instance of the pRT class, with optical properties as defined in the RunDefinition.

parametersdict
Dictionary of required parameters:

  • D_pl : Distance to the planet in [cm]

Two of

  • log_g : Log of surface gravity

  • planet_radius : planet radius [cm]

  • mass : planet mass [g]

  • T_int : Interior temperature of the planet [K]

  • T3 : Innermost temperature spline [K]

  • T2 : Middle temperature spline [K]

  • T1 : Outer temperature spline [K]

  • alpha : power law index in tau = delta * press_cgs**alpha

  • log_delta : proportionality factor in tau = delta * press_cgs**alpha

  • log_pquench : Pressure at which CO, CH4 and H2O abundances become vertically constant

  • Fe/H : Metallicity

  • C/O : Carbon to oxygen ratio

  • fsed : sedimentation parameter - can be unique to each cloud type by adding _CloudName

One of:

  • sigma_lnorm : Width of cloud particle size distribution (log normal)

  • b_hans : Width of cloud particle size distribution (hansen)

One of:

  • log_cloud_radius_* : Central particle radius (typically computed with fsed and Kzz)

  • log_kzz : Vertical mixing parameter

One of

  • eq_scaling_* : Scaling factor for equilibrium cloud abundances.

  • log_X_cb_: cloud mass fraction abundance

Optional

  • contribution : return the emission contribution function

  • patchiness : Cloud coverage fraction, mixes two columns with different cloud properties.

  • remove_cloud_species : Specifies which cloud species to remove for clear atmosphere column.

  • T_disk_blackbody : Temperature of a blackbody circumplanetary disk component.

  • disk_radius : Radius [cm] of a blackbody circumplanetary disk component.

pt_plot_modebool

Return only the pressure-temperature profile for plotting. Evaluate mode only.

amrbool

Adaptive mesh refinement. Use the high resolution pressure grid around the cloud base.

Returns:
wlen_modelnp.ndarray

Wavlength array of computed model, not binned to data [um]

spectrum_modelnp.ndarray

Computed emission spectrum [W/m2/micron]

contr_emOptional, np.ndarray

Emission contribution function, relative contributions for each wavelength and pressure level.

petitRADTRANS.retrieval.models.emission_model_diseq_simple_patchy_clouds(prt_object, parameters, pt_plot_mode=False, amr=True)#

Deprecated, to be removed in future version

petitRADTRANS.retrieval.models.emission_model_diseq_patchy_clouds(prt_object, parameters, pt_plot_mode=False, amr=True)#

Disequilibrium Chemistry Emission Model

This model computes an emission spectrum based on the temperature profile of (Molliere 2020). (Dis)equilibrium or free chemistry, can be used. The use of easychem for on-the-fly (dis)equilibrium chemistry calculations is supported, but is currently under development. This model includes patchy clouds, and requires a unique temperature profile for the clear atmosphere regions - ie this is a full two column model!

Args:
prt_objectobject

An instance of the pRT class, with optical properties as defined in the RunDefinition.

parametersdict
Dictionary of required parameters:

  • D_pl : Distance to the planet in [cm]

Two of

  • log_g : Log of surface gravity

  • planet_radius : planet radius [cm]

  • mass : planet mass [g]

  • T_int : Interior temperature of the planet [K]

  • T3 : Innermost temperature spline

  • T2 : Middle temperature spline

  • T1 : Outer temperature spline

  • T3_clear : Innermost temperature spline for clear atmosphere

  • T2_clear : Middle temperature spline for clear atmosphere

  • T1_clear : Outer temperature spline for clear atmosphere

  • alpha : power law index in tau = delta * press_cgs**alpha

  • alpha_clear : power law index in tau = delta * press_cgs**alpha for clear atmosphere

  • log_delta : proportionality factor in tau = delta * press_cgs**alpha

  • log_delta_clear : proportionality factor in tau = delta * press_cgs**alpha for clear atmosphere

  • log_pquench : Pressure at which CO, CH4 and H2O abundances become vertically constant

  • Fe/H : Metallicity

  • C/O : Carbon to oxygen ratio

  • fsed : sedimentation parameter - can be unique to each cloud type

One of:

  • sigma_lnorm : Width of cloud particle size distribution (log normal)

  • b_hans : Width of cloud particle size distribution (hansen)

One of:

  • log_cloud_radius_* : Central particle radius (typically computed with fsed and Kzz)

  • log_kzz : Vertical mixing parameter

One of

  • eq_scaling_* : Scaling factor for equilibrium cloud abundances.

  • log_X_cb_: cloud mass fraction abundance

Optional

  • contribution : return the emission contribution function

  • patchiness : Cloud coverage fraction, mixes two columns with different cloud properties.

  • remove_cloud_species : Specifies which cloud species to remove for the clear atmosphere column.

  • T_disk_blackbody : Temperature of a blackbody circumplanetary disk component.

  • disk_radius : Radius [cm] of a blackbody circumplanetary disk component.

pt_plot_modebool

Return only the pressure-temperature profile for plotting. Evaluate mode only.

amrbool

Adaptive mesh refinement. Use the high resolution pressure grid around the cloud base.

Returns:
wlen_modelnp.array

Wavlength array of computed model, not binned to data [um]

spectrum_modelnp.array

Computed emission spectrum [W/m2/micron]

contr_emOptional, np.ndarray

Emission contribution function, relative contributions for each wavelength and pressure level. Only returns the contribution of the clear atmosphere component.

petitRADTRANS.retrieval.models.guillot_emission(prt_object, parameters, pt_plot_mode=False, amr=False)#

Emission spectrum calculation for the Guillot 2010 temperature profile. (Dis)equilibrium or free chemistry, can be used. The use of easychem for on-the-fly (dis)equilibrium chemistry calculations is supported, but is currently under development.

Args:
prt_objectobject

An instance of the pRT class, with optical properties as defined in the RunDefinition.

parametersdict
Dictionary of required parameters:

  • D_pl : Distance to the planet in [cm]

Two of

  • log_g : Log of surface gravity

  • planet_radius : planet radius [cm]

  • mass : planet mass [g]

  • T_int : Interior temperature of the planet [K]

  • T_equ : Equilibrium temperature of the planet

  • gamma : Guillot gamma parameter

  • log_kappa_IR : The log of the ratio between the infrared and optical opacities

Either:

  • log_pquench : Pressure at which CO, CH4 and H2O abundances become vertically constant

  • Fe/H : Metallicity

  • C/O : Carbon to oxygen ratio

Or:

  • $SPECIESNAME[_$DATABASE][_R_$RESOLUTION] : The log mass fraction abundance of the species

  • fsed : sedimentation parameter - can be unique to each cloud type

One of:

  • sigma_lnorm : Width of cloud particle size distribution (log normal)

  • b_hans : Width of cloud particle size distribution (hansen)

One of:

  • log_cloud_radius_* : Central particle radius (typically computed with fsed and Kzz)

  • log_kzz : Vertical mixing parameter

One of

  • eq_scaling_* : Scaling factor for equilibrium cloud abundances.

  • log_X_cb_: cloud mass fraction abundance

Optional

  • contribution : return the emission contribution function

  • patchiness : Cloud coverage fraction, mixes two columns with different cloud properties.

  • remove_cloud_species : Specifies which cloud species to remove for the clear atmosphere column.

  • T_disk_blackbody : Temperature of a blackbody circumplanetary disk component.

  • disk_radius : Radius [cm] of a blackbody circumplanetary disk component.

pt_plot_modebool

Return only the pressure-temperature profile for plotting. Evaluate mode only.

amr :

Adaptive mesh refinement. Use the high resolution pressure grid around the cloud base.

Returns:
wlen_modelnp.array

Wavlength array of computed model, not binned to data [um]

spectrum_modelnp.array

Computed transmission spectrum planet_radius**2/Rstar**2

contr-emnp.ndarray

Optional, Emission contribution function, relative contributions for each wavelength and pressure level.

petitRADTRANS.retrieval.models.guillot_emission_add_gaussian_temperature(prt_object, parameters, pt_plot_mode=False, amr=False)#

Emission spectrum calculation for the Guillot 2010 temperature profile. (Dis)equilibrium or free chemistry, can be used. The use of easychem for on-the-fly (dis)equilibrium chemistry calculations is supported, but is currently under development.

Args:
prt_objectobject

An instance of the pRT class, with optical properties as defined in the RunDefinition.

parametersdict
Dictionary of required parameters:

  • D_pl : Distance to the planet in [cm]

Two of

  • log_g : Log of surface gravity

  • planet_radius : planet radius [cm]

  • mass : planet mass [g]

  • T_int : Interior temperature of the planet [K]

  • T_equ : Equilibrium temperature of the planet

  • gamma : Guillot gamma parameter

  • log_kappa_IR : The log of the ratio between the infrared and optical opacities

Either:

  • log_pquench : Pressure at which CO, CH4 and H2O abundances become vertically constant

  • Fe/H : Metallicity

  • C/O : Carbon to oxygen ratio

Or:

  • $SPECIESNAME[_$DATABASE][_R_$RESOLUTION] : The log mass fraction abundance of the species

  • fsed : sedimentation parameter - can be unique to each cloud type

One of:

  • sigma_lnorm : Width of cloud particle size distribution (log normal)

  • b_hans : Width of cloud particle size distribution (hansen)

One of:

  • log_cloud_radius_* : Central particle radius (typically computed with fsed and Kzz)

  • log_kzz : Vertical mixing parameter

One of

  • eq_scaling_* : Scaling factor for equilibrium cloud abundances.

  • log_X_cb_: cloud mass fraction abundance

Optional

  • contribution : return the emission contribution function

  • patchiness : Cloud coverage fraction, mixes two columns with different cloud properties.

  • remove_cloud_species : Specifies which cloud species to remove for the clear atmosphere column.

  • T_disk_blackbody : Temperature of a blackbody circumplanetary disk component.

  • disk_radius : Radius [cm] of a blackbody circumplanetary disk component.

pt_plot_modebool

Return only the pressure-temperature profile for plotting. Evaluate mode only.

amr :

Adaptive mesh refinement. Use the high resolution pressure grid around the cloud base.

Returns:
wlen_modelnp.array

Wavlength array of computed model, not binned to data [um]

spectrum_modelnp.array

Computed transmission spectrum planet_radius**2/Rstar**2

contr-emnp.ndarray

Optional, Emission contribution function, relative contributions for each wavelength and pressure level.

petitRADTRANS.retrieval.models.guillot_patchy_emission(prt_object, parameters, pt_plot_mode=False, amr=False)#

Deprecated, to be removed in future version

petitRADTRANS.retrieval.models.interpolated_profile_emission(prt_object, parameters, pt_plot_mode=False, amr=False)#

This model computes a emission spectrum based a spline temperature-pressure profile. Either free or equilibrium chemistry can be used, together with a range of cloud parameterizations. It is possible to use free abundances for some species and equilibrium chemistry for the remainder.

Args:
prt_objectobject

An instance of the pRT class, with optical properties as defined in the RunDefinition.

parametersdict
Dictionary of required parameters:

  • D_pl : Distance to the planet in [cm]

Two of

  • log_g : Log of surface gravity

  • planet_radius : planet radius [cm]

  • mass : planet mass [g]

  • nnodesnumber of nodes to interplate, excluding the first and last points.

    so the total number of nodes is nnodes + 2

  • T{i} : One parameter for each temperature node

  • gamma : weight for penalizing the profile curvature

Either:

  • log_pquench : Pressure at which CO, CH4 and H2O abundances become vertically constant

  • Fe/H : Metallicity

  • C/O : Carbon to oxygen ratio

Or:

  • $SPECIESNAME[_$DATABASE][_R_$RESOLUTION] : The log mass fraction abundance of the species

Optional: * fsed : sedimentation parameter - can be unique to each cloud type One of:

  • sigma_lnorm : Width of cloud particle size distribution (log normal)

  • b_hans : Width of cloud particle size distribution (hansen)

One of:

  • log_cloud_radius_* : Central particle radius (typically computed with fsed and Kzz)

  • log_kzz : Vertical mixing parameter

One of

  • eq_scaling_* : Scaling factor for equilibrium cloud abundances.

  • log_X_cb_: cloud mass fraction abundance

Optional

  • contribution : return the emission contribution function

  • patchiness : Cloud coverage fraction, mixes two columns with different cloud properties.

  • remove_cloud_species : Specifies which cloud species to remove for the clear atmosphere column.

  • T_disk_blackbody : Temperature of a blackbody circumplanetary disk component.

  • disk_radius : Radius [cm] of a blackbody circumplanetary disk component.

pt_plot_modebool

Return only the pressure-temperature profile for plotting. Evaluate mode only.

amr :

Adaptive mesh refinement. Use the high resolution pressure grid around the cloud base.

Returns:
wlen_modelnp.array

Wavlength array of computed model, not binned to data [um]

spectrum_modelnp.array

Computed transmission spectrum planet_radius**2/Rstar**2

contr-emnp.ndarray

Optional, the emission contribution function, relative contributions for each wavelength and pressure level.

petitRADTRANS.retrieval.models.gradient_profile_emission(prt_object, parameters, pt_plot_mode=False, amr=False)#

This model computes a emission spectrum based a gradient temperature-pressure profile (Zhang 2023). Either free or equilibrium chemistry can be used, together with a range of cloud parameterizations. It is possible to use free abundances for some species and equilibrium chemistry for the remainder.

Args:
prt_objectobject

An instance of the pRT class, with optical properties as defined in the RunDefinition.

parametersdict
Dictionary of required parameters:

  • D_pl : Distance to the planet in [cm]

Two of

  • log_g : Log of surface gravity

  • planet_radius : planet radius [cm]

  • mass : planet mass [g]

  • N_layersnumber of nodes to interplate, excluding the first and last points.

    so the total number of nodes is nnodes + 2

  • T_bottom : temperature at the base of the atmosphere

  • PTslope_* : temperature gradient for each of the n_layers between which the profile is interpolated.

Either:

  • log_pquench : Pressure at which CO, CH4 and H2O abundances become vertically constant

  • Fe/H : Metallicity

  • C/O : Carbon to oxygen ratio

Or:

  • $SPECIESNAME[_$DATABASE][_R_$RESOLUTION] : The log mass fraction abundance of the species

Optional: * fsed : sedimentation parameter - can be unique to each cloud type One of:

  • sigma_lnorm : Width of cloud particle size distribution (log normal)

  • b_hans : Width of cloud particle size distribution (hansen)

One of:

  • log_cloud_radius_* : Central particle radius (typically computed with fsed and Kzz)

  • log_kzz : Vertical mixing parameter

One of

  • eq_scaling_* : Scaling factor for equilibrium cloud abundances.

  • log_X_cb_: cloud mass fraction abundance

Optional

  • contribution : return the emission contribution function

  • patchiness : Cloud coverage fraction, mixes two columns with different cloud properties.

  • remove_cloud_species : Specifies which cloud species to remove for the clear atmosphere column.

  • T_disk_blackbody : Temperature of a blackbody circumplanetary disk component.

  • disk_radius : Radius [cm] of a blackbody circumplanetary disk component.

pt_plot_modebool

Return only the pressure-temperature profile for plotting. Evaluate mode only.

amr :

Adaptive mesh refinement. Use the high resolution pressure grid around the cloud base.

Returns:
wlen_modelnp.array

Wavlength array of computed model, not binned to data [um]

spectrum_modelnp.array

Computed transmission spectrum planet_radius**2/Rstar**2

contr-emnp.ndarray

Optional, the emission contribution function, relative contributions for each wavelength and pressure level.

petitRADTRANS.retrieval.models.power_law_profile_emission(prt_object, parameters, pt_plot_mode=False, amr=False)#

This model computes a emission spectrum based a gradient temperature-pressure profile (Zhang 2023). Either free or equilibrium chemistry can be used, together with a range of cloud parameterizations. It is possible to use free abundances for some species and equilibrium chemistry for the remainder.

Args:
prt_objectobject

An instance of the pRT class, with optical properties as defined in the RunDefinition.

parametersdict
Dictionary of required parameters:

  • D_pl : Distance to the planet in [cm]

Two of

  • log_g : Log of surface gravity

  • planet_radius : planet radius [cm]

  • mass : planet mass [g]

  • alpha : power law slope for the temperture profile

  • T_0 : multiplicative factor for the power law slope

Either:

  • log_pquench : Pressure at which CO, CH4 and H2O abundances become vertically constant

  • Fe/H : Metallicity

  • C/O : Carbon to oxygen ratio

Or:

  • $SPECIESNAME[_$DATABASE][_R_$RESOLUTION] : The log mass fraction abundance of the species

Optional: * fsed : sedimentation parameter - can be unique to each cloud type One of:

  • sigma_lnorm : Width of cloud particle size distribution (log normal)

  • b_hans : Width of cloud particle size distribution (hansen)

One of:

  • log_cloud_radius_* : Central particle radius (typically computed with fsed and Kzz)

  • log_kzz : Vertical mixing parameter

One of

  • eq_scaling_* : Scaling factor for equilibrium cloud abundances.

  • log_X_cb_: cloud mass fraction abundance

Optional

  • contribution : return the emission contribution function

  • patchiness : Cloud coverage fraction, mixes two columns with different cloud properties.

  • remove_cloud_species : Specifies which cloud species to remove for the clear atmosphere column.

  • T_disk_blackbody : Temperature of a blackbody circumplanetary disk component.

  • disk_radius : Radius [cm] of a blackbody circumplanetary disk component.

pt_plot_modebool

Return only the pressure-temperature profile for plotting. Evaluate mode only.

amr :

Adaptive mesh refinement. Use the high resolution pressure grid around the cloud base.

Returns:
wlen_modelnp.array

Wavlength array of computed model, not binned to data [um]

spectrum_modelnp.array

Computed transmission spectrum planet_radius**2/Rstar**2

contr-emnp.ndarray

Optional, the emission contribution function, relative contributions for each wavelength and pressure level.

petitRADTRANS.retrieval.models.guillot_transmission(prt_object, parameters, pt_plot_mode=False, amr=False)#

Transmission Model, Guillot Profile

This model computes a transmission spectrum based on the Guillot profile Either free or (dis)equilibrium chemistry can be used, together with a range of cloud parameterizations. It is possible to use free abundances for some species and equilibrium chemistry for the remainder. Chemical clouds can be used, or a simple gray opacity source.

Args:
prt_objectobject

An instance of the pRT class, with optical properties as defined in the RunDefinition.

parametersdict
Dictionary of required parameters:

  • D_pl : Distance to the planet in [cm]

Two of

  • log_g : Log of surface gravity

  • planet_radius : planet radius [cm]

  • mass : planet mass [g]

  • T_int : Interior temperature of the planet [K]

  • T_equ : Equilibrium temperature of the planet

  • gamma : Guillot gamma parameter

  • log_kappa_IR : The log of the ratio between the infrared and optical opacities

Either:

  • log_pquench : Pressure at which CO, CH4 and H2O abundances become vertically constant

  • Fe/H : Metallicity

  • C/O : Carbon to oxygen ratio

Or:

  • $SPECIESNAME[_$DATABASE][.R$RESOLUTION] : The log mass fraction abundance of the species

Either:

  • [log_]Pcloud : The (log) pressure at which to place the gray cloud opacity.

Or:

  • fsed : sedimentation parameter - can be unique to each cloud type

One of:

  • sigma_lnorm : Width of cloud particle size distribution (log normal)

  • b_hans : Width of cloud particle size distribution (hansen)

One of:

  • log_cloud_radius_* : Central particle radius (typically computed with fsed and Kzz)

  • log_kzz : Vertical mixing parameter

One of

  • eq_scaling_* : Scaling factor for equilibrium cloud abundances.

  • log_X_cb_: cloud mass fraction abundance

Optional

  • contribution : return the transmission contribution function

  • power_law_opacity_coefficient : gamma, power law slope for a rayleigh-like haze

  • haze_factor : multiplicative scaling factor for the strength of the rayleigh haze

  • power_law_opacity_350nm : strength of the rayleigh haze at 350 nm.

pt_plot_modebool

Return only the pressure-temperature profile for plotting. Evaluate mode only.

amr :

Adaptive mesh refinement. Use the high resolution pressure grid around the cloud base.

Returns:
wlen_modelnp.array

Wavlength array of computed model, not binned to data [um]

spectrum_modelnp.array

Computed transmission spectrum planet_radius**2/Rstar**2

contr-emnp.ndarray

Optional, the transmission contribution function, relative contributions for each wavelength and pressure level.

petitRADTRANS.retrieval.models.guillot_patchy_transmission(prt_object, parameters, pt_plot_mode=False, amr=False)#

Deprecated

petitRADTRANS.retrieval.models.madhushudhan_seager_emission(prt_object, parameters, pt_plot_mode=False, amr=False)#

Transmission Model, Madhusudhan Seager 2009 Profile

This model computes a transmission spectrum based on a Guillot temperature-pressure profile. Either free or equilibrium chemistry can be used, together with a range of cloud parameterizations. It is possible to use free abundances for some species and equilibrium chemistry for the remainder. Chemical clouds can be used, or a simple gray opacity source. This model requires patchy clouds.

Args:
prt_objectobject

An instance of the pRT class, with optical properties as defined in the RunDefinition.

parametersdict
Dictionary of required parameters:

  • D_pl : Distance to the planet in [cm]

Two of

  • log_g : Log of surface gravity

  • planet_radius : planet radius [cm]

  • mass : planet mass [g]

  • log_P_set : Pressure value to contrain the PT profile, defaults to 10 bar.

  • T_set : temperature at P_set to constrain the PT profile. [K]

  • log_P3 : (log) Pressure value for the top of the deep atmospheric layer, [bar]

  • P2 : in range (0,1), sets the pressure level of the middle atmospheric layer

  • P1 : in range (0,1), sets the pressure level of the top atmospheric layer

  • alpha_0 : slope of the upper atmospheric layer

  • alpha_1 : slope of the middle atmospheric layer

Optional :

  • beta : power law for the slopes, default value is 0.5. Not recommended to change!

Either:

  • log_pquench : Pressure at which CO, CH4 and H2O abundances become vertically constant

  • Fe/H : Metallicity

  • C/O : Carbon to oxygen ratio

Or:

  • $SPECIESNAME[_$DATABASE][.R$RESOLUTION] : The log mass fraction abundance of the species

Optional: * fsed : sedimentation parameter - can be unique to each cloud type One of:

  • sigma_lnorm : Width of cloud particle size distribution (log normal)

  • b_hans : Width of cloud particle size distribution (hansen)

One of:

  • log_cloud_radius_* : Central particle radius (typically computed with fsed and Kzz)

  • log_kzz : Vertical mixing parameter

One of

  • eq_scaling_* : Scaling factor for equilibrium cloud abundances.

  • log_X_cb_: cloud mass fraction abundance

Optional

  • contribution : return the emission contribution function

  • patchiness : Cloud coverage fraction, mixes two columns with different cloud properties.

  • remove_cloud_species : Specifies which cloud species to remove for the clear atmosphere column.

  • T_disk_blackbody : Temperature of a blackbody circumplanetary disk component.

  • disk_radius : Radius [cm] of a blackbody circumplanetary disk component.

pt_plot_modebool

Return only the pressure-temperature profile for plotting. Evaluate mode only.

amr :

Adaptive mesh refinement. Use the high resolution pressure grid around the cloud base.

Returns:
wlen_modelnp.array

Wavlength array of computed model, not binned to data [um]

spectrum_modelnp.array

Computed transmission spectrum planet_radius**2/Rstar**2

contr-emnp.ndarray

Optional, the transmission contribution function, relative contributions for each wavelength and pressure level. Only the clear atmosphere contribution is returned.

petitRADTRANS.retrieval.models.madhushudhan_seager_transmission(prt_object, parameters, pt_plot_mode=False, amr=False)#

Transmission Model, Madhusudhan Seager 2009 Profile

This model computes a transmission spectrum based on a Guillot temperature-pressure profile. Either free or equilibrium chemistry can be used, together with a range of cloud parameterizations. It is possible to use free abundances for some species and equilibrium chemistry for the remainder. Chemical clouds can be used, or a simple gray opacity source. This model requires patchy clouds.

Args:
prt_objectobject

An instance of the pRT class, with optical properties as defined in the RunDefinition.

parametersdict
Dictionary of required parameters:

  • D_pl : Distance to the planet in [cm]

Two of

  • log_g : Log of surface gravity

  • planet_radius : planet radius [cm]

  • mass : planet mass [g]

  • log_P_set : Pressure value to contrain the PT profile, defaults to 10 bar.

  • T_set : temperature at P_set to constrain the PT profile. [K]

  • log_P3 : (log) Pressure value for the top of the deep atmospheric layer, [bar]

  • P2 : in range (0,1), sets the pressure level of the middle atmospheric layer

  • P1 : in range (0,1), sets the pressure level of the top atmospheric layer

  • alpha_0 : slope of the upper atmospheric layer

  • alpha_1 : slope of the middle atmospheric layer

Optional :

  • beta : power law for the slopes, default value is 0.5. Not recommended to change!

Either:

  • log_pquench : Pressure at which CO, CH4 and H2O abundances become vertically constant

  • Fe/H : Metallicity

  • C/O : Carbon to oxygen ratio

Or:

  • $SPECIESNAME[_$DATABASE][.R$RESOLUTION] : The log mass fraction abundance of the species

Either:

  • [log_]Pcloud : The (log) pressure at which to place the gray cloud opacity.

Or:

  • fsed : sedimentation parameter - can be unique to each cloud type

One of:

  • sigma_lnorm : Width of cloud particle size distribution (log normal)

  • b_hans : Width of cloud particle size distribution (hansen)

One of:

  • log_cloud_radius_* : Central particle radius (typically computed with fsed and Kzz)

  • log_kzz : Vertical mixing parameter

One of

  • eq_scaling_* : Scaling factor for equilibrium cloud abundances.

  • log_X_cb_: cloud mass fraction abundance

Optional

  • contribution : return the transmission contribution function

  • power_law_opacity_coefficient : gamma, power law slope for a rayleigh-like haze

  • haze_factor : multiplicative scaling factor for the strength of the rayleigh haze

  • power_law_opacity_350nm : strength of the rayleigh haze at 350 nm.

pt_plot_modebool

Return only the pressure-temperature profile for plotting. Evaluate mode only.

amr :

Adaptive mesh refinement. Use the high resolution pressure grid around the cloud base.

Returns:
wlen_modelnp.array

Wavlength array of computed model, not binned to data [um]

spectrum_modelnp.array

Computed transmission spectrum planet_radius**2/Rstar**2

contr-emnp.ndarray

Optional, the transmission contribution function, relative contributions for each wavelength and pressure level. Only the clear atmosphere contribution is returned.

petitRADTRANS.retrieval.models.madhu_seager_patchy_transmission(prt_object, parameters, pt_plot_mode=False, amr=False)#

Deprecated

petitRADTRANS.retrieval.models.isothermal_transmission(prt_object, parameters, pt_plot_mode=False, amr=False)#

Equilibrium Chemistry Transmission Model, Isothermal Profile

This model computes a transmission spectrum based on an isothermal temperature-pressure profile.

Args:
prt_objectobject

An instance of the pRT class, with optical properties as defined in the RunDefinition.

parametersdict
Dictionary of required parameters:

  • D_pl : Distance to the planet in [cm]

Two of

  • log_g : Log of surface gravity

  • planet_radius : planet radius [cm]

  • mass : planet mass [g]

  • temperature : Interior temperature of the planet [K]

Either:

  • log_pquench : Pressure at which CO, CH4 and H2O abundances become vertically constant

  • Fe/H : Metallicity

  • C/O : Carbon to oxygen ratio

Or:

  • $SPECIESNAME[_$DATABASE][.R$RESOLUTION] : The log mass fraction abundance of the species

Either:

  • [log_]Pcloud : The (log) pressure at which to place the gray cloud opacity.

Or:

  • fsed : sedimentation parameter - can be unique to each cloud type

One of:

  • sigma_lnorm : Width of cloud particle size distribution (log normal)

  • b_hans : Width of cloud particle size distribution (hansen)

One of:

  • log_cloud_radius_* : Central particle radius (typically computed with fsed and Kzz)

  • log_kzz : Vertical mixing parameter

One of

  • eq_scaling_* : Scaling factor for equilibrium cloud abundances.

  • log_X_cb_: cloud mass fraction abundance

Optional

  • contribution : return the transmission contribution function

  • power_law_opacity_coefficient : gamma, power law slope for a rayleigh-like haze

  • haze_factor : multiplicative scaling factor for the strength of the rayleigh haze

  • power_law_opacity_350nm : strength of the rayleigh haze at 350 nm.

pt_plot_modebool

Return only the pressure-temperature profile for plotting. Evaluate mode only.

amr :

Adaptive mesh refinement. Use the high resolution pressure grid around the cloud base.

Returns:
wlen_modelnp.array

Wavlength array of computed model, not binned to data [um]

spectrum_modelnp.array

Computed transmission spectrum planet_radius**2/Rstar**2

contr-emnp.ndarray

Optional, the transmission contribution function, relative contributions for each wavelength and pressure level. Only the clear atmosphere contribution is returned if patchy clouds are considered.

petitRADTRANS.retrieval.models.power_law_profile_transmission(prt_object, parameters, pt_plot_mode=False, amr=False)#

This model computes a emission spectrum based a gradient temperature-pressure profile (Zhang 2023). Either free or equilibrium chemistry can be used, together with a range of cloud parameterizations. It is possible to use free abundances for some species and equilibrium chemistry for the remainder.

Args:
prt_objectobject

An instance of the pRT class, with optical properties as defined in the RunDefinition.

parametersdict
Dictionary of required parameters:

  • D_pl : Distance to the planet in [cm]

Two of

  • log_g : Log of surface gravity

  • planet_radius : planet radius [cm]

  • mass : planet mass [g]

  • alpha : power law slope for the temperture profile

  • T_0 : multiplicative factor for the power law slope

Either:

  • log_pquench : Pressure at which CO, CH4 and H2O abundances become vertically constant

  • Fe/H : Metallicity

  • C/O : Carbon to oxygen ratio

Or:

  • $SPECIESNAME[_$DATABASE][_R_$RESOLUTION] : The log mass fraction abundance of the species

Optional: * fsed : sedimentation parameter - can be unique to each cloud type One of:

  • sigma_lnorm : Width of cloud particle size distribution (log normal)

  • b_hans : Width of cloud particle size distribution (hansen)

One of:

  • log_cloud_radius_* : Central particle radius (typically computed with fsed and Kzz)

  • log_kzz : Vertical mixing parameter

One of

  • eq_scaling_* : Scaling factor for equilibrium cloud abundances.

  • log_X_cb_: cloud mass fraction abundance

Optional

  • contribution : return the emission contribution function

  • patchiness : Cloud coverage fraction, mixes two columns with different cloud properties.

  • remove_cloud_species : Specifies which cloud species to remove for the clear atmosphere column.

  • T_disk_blackbody : Temperature of a blackbody circumplanetary disk component.

  • disk_radius : Radius [cm] of a blackbody circumplanetary disk component.

pt_plot_modebool

Return only the pressure-temperature profile for plotting. Evaluate mode only.

amr :

Adaptive mesh refinement. Use the high resolution pressure grid around the cloud base.

Returns:
wlen_modelnp.array

Wavlength array of computed model, not binned to data [um]

spectrum_modelnp.array

Computed transmission spectrum planet_radius**2/Rstar**2

contr-emnp.ndarray

Optional, the emission contribution function, relative contributions for each wavelength and pressure level.

petitRADTRANS.retrieval.models.add_blackbody_cpd_model(parameters, wavelengths)#

Calculates the flux of a blackbody with area 4*pi*disk_radius^2 and temperature T_disk_blackbody. This is in units of W/m2/micron, and can be added to a planetary spectrum to model the contribution of a circumplanetary disk

Args:

parameters (dict): dictionary of atmospheric and disk parameters wavelengths (np.ndarray): Wavelength grid of atmospheric model in micron

Returns:

blackbody_spectrum (np.ndarray): 1D Planck emission spectrum for a circular CPD.

petitRADTRANS.retrieval.models.initialize_pressure(press, parameters, amr)#

Provide the pressure array correctly sized to the prt_object in use, accounting for the use of Adaptive Mesh Refinement around the location of clouds.

Args:
pressnumpy.ndarray

Pressure array from a prt_object. Used to set the min and max values of PGLOBAL

parameters :

# TODO complete docstring

amr :

# TODO complete docstring

petitRADTRANS.retrieval.models.set_pglobal(press, parameters)#

Check to ensure that the global pressure array has the correct length. Updates PGLOBAL.

Args:
pressnumpy.ndarray

Pressure array from a prt_object. Used to set the min and max values of PGLOBAL

parametersdict

Must include the ‘pressure_simple’ and ‘pressure_scaling’ parameters, used to determine the size of the high resolution grid.

petitRADTRANS.retrieval.models.calculate_emission_spectrum(prt_object, parameters, temperatures, abundances, gravity, mean_molar_masses, planet_radius, sigma_lnorm, cloud_particles_mean_radii, cloud_f_sed, eddy_diffusion_coefficients, cloud_hansen_b, cloud_fraction, complete_coverage_clouds, distribution)#

Calls Radtrans.calculate_flux to compute the emission spectrum of an atmosphere. This function automatically checks if patchiness is included in the retrieval, and mixes the clear and cloudy columns. Patchiness can be applied to all of the cloud species, or individual clouds can be chosen using the remove_cloud_species parameter. A circumplanetary disk model is optionally included, modelled as a blackbody with some temperature T_disk_blackbody and a radius disk_radius.

Args:

prt_object (Radtrans): The Radtrans object used to calculate the spectrum parameters (dict): Dictionary of atmospheric parameters. temperatures (np.ndarray): Array of temperatures for each pressure level in the atmosphere abundances (dict): Dictionary of molecular mass fraction abundances for each level in the atmosphere gravity (np.ndarray): Gravitational acceleration at each pressure level mean_molar_masses (np.ndarray): Mean molecular mass at each pressure level planet_radius (float): Planet radius in cm sigma_lnorm (float): Width of the cloud particle size distribution (log-normal) cloud_particles_mean_radii (np.ndarray): Mean particle radius cloud_f_sed (np.ndarray): Sedimentation fraction eddy_diffusion_coefficients (np.ndarray): Vertical mixing strength (Kzz) cloud_hansen_b (np.ndarray): Cloud particle distribution width, hansen distsribution cloud_fraction (float) : fraction of planet covered by clouds complete_coverage_clouds (list(str)) : Which clouds are NOT patchy distribution (string): Which cloud particle size distribution to use

petitRADTRANS.retrieval.models.calculate_transmission_spectrum(prt_object, parameters, temperatures, abundances, gravity, mean_molar_masses, planet_radius, reference_pressure, opaque_cloud_top_pressure, sigma_lnorm, cloud_particles_mean_radii, cloud_f_sed, eddy_diffusion_coefficients, haze_factor, power_law_opacity_coefficient, power_law_opacity_350nm, cloud_hansen_b, cloud_fraction, complete_coverage_clouds, distribution)#

_summary_

Args:

prt_object (Radtrans): The Radtrans object used to calculate the spectrum parameters (dict): Dictionary of atmospheric parameters. temperatures (np.ndarray): Array of temperatures for each pressure level in the atmosphere abundances (dict): Dictionary of molecular mass fraction abundances for each level in the atmosphere gravity (np.ndarray): Gravitational acceleration at each pressure level mean_molar_masses (np.ndarray): Mean molecular mass at each pressure level planet_radius (float):Planet radius in cm reference_pressure (float): Pressure at which the planet radius is defined opaque_cloud_top_pressure (float): Pressure where an opaque grey cloud deck is placed sigma_lnorm (float): Width of the cloud particle size distribution (log-normal) cloud_particles_mean_radii (np.ndarray): Mean particle radius cloud_f_sed (np.ndarray): Sedimentation fraction eddy_diffusion_coefficients (np.ndarray): Vertical mixing strength (Kzz) haze_factor (float): Multiplicative factor on the strength of a power law haze slope power_law_opacity_coefficient (float): Exponent for the slope of a power law haze power_law_opacity_350nm (float): Strength of the power law scattering at 350nm cloud_hansen_b (np.ndarray): Cloud particle distribution width, hansen distsribution cloud_fraction (float) : fraction of planet covered by clouds complete_coverage_clouds (list(str)) : Which clouds are NOT patchy distribution (string): Log normal or hansen particle size distribution

Returns:

_type_: _description_

petitRADTRANS.retrieval.models.pglobal_check(press, shape, scaling)#

Check to ensure that the global pressure array has the correct length. Updates PGLOBAL.

Args:
pressnumpy.ndarray

Pressure array from a prt_object. Used to set the min and max values of PGLOBAL

shapeint

the shape of the pressure array if no amr is used

scaling :

The factor by which the pressure array resolution should be scaled.