petitRADTRANS.retrieval.models ============================== .. py:module:: petitRADTRANS.retrieval.models .. autoapi-nested-parse:: 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_object : petitRADTRANS.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 parameters : dict 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_mode : bool If this argument is True, the model function should return the pressure and temperature arrays before computing the flux. amr : bool 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 ---------- .. autoapisummary:: petitRADTRANS.retrieval.models.PGLOBAL Functions --------- .. autoapisummary:: petitRADTRANS.retrieval.models._compute_gravity petitRADTRANS.retrieval.models.emission_model_diseq petitRADTRANS.retrieval.models.emission_model_diseq_simple_patchy_clouds petitRADTRANS.retrieval.models.emission_model_diseq_patchy_clouds petitRADTRANS.retrieval.models.guillot_emission petitRADTRANS.retrieval.models.guillot_emission_add_gaussian_temperature petitRADTRANS.retrieval.models.guillot_patchy_emission petitRADTRANS.retrieval.models.interpolated_profile_emission petitRADTRANS.retrieval.models.gradient_profile_emission petitRADTRANS.retrieval.models.power_law_profile_emission petitRADTRANS.retrieval.models.guillot_transmission petitRADTRANS.retrieval.models.guillot_patchy_transmission petitRADTRANS.retrieval.models.madhushudhan_seager_emission petitRADTRANS.retrieval.models.madhushudhan_seager_transmission petitRADTRANS.retrieval.models.madhu_seager_patchy_transmission petitRADTRANS.retrieval.models.isothermal_transmission petitRADTRANS.retrieval.models.power_law_profile_transmission petitRADTRANS.retrieval.models.add_blackbody_cpd_model petitRADTRANS.retrieval.models.initialize_pressure petitRADTRANS.retrieval.models.set_pglobal petitRADTRANS.retrieval.models.calculate_emission_spectrum petitRADTRANS.retrieval.models.calculate_transmission_spectrum petitRADTRANS.retrieval.models.pglobal_check Module Contents --------------- .. py:data:: PGLOBAL .. py:function:: _compute_gravity(parameters) .. py:function:: 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_object : object An instance of the pRT class, with optical properties as defined in the RunDefinition. parameters : dict 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_mode : bool Return only the pressure-temperature profile for plotting. Evaluate mode only. amr : bool Adaptive mesh refinement. Use the high resolution pressure grid around the cloud base. Returns: wlen_model : np.ndarray Wavlength array of computed model, not binned to data [um] spectrum_model : np.ndarray Computed emission spectrum [W/m2/micron] contr_em : Optional, np.ndarray Emission contribution function, relative contributions for each wavelength and pressure level. .. py:function:: emission_model_diseq_simple_patchy_clouds(prt_object, parameters, pt_plot_mode=False, amr=True) Deprecated, to be removed in future version .. py:function:: 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_object : object An instance of the pRT class, with optical properties as defined in the RunDefinition. parameters : dict 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_mode : bool Return only the pressure-temperature profile for plotting. Evaluate mode only. amr : bool Adaptive mesh refinement. Use the high resolution pressure grid around the cloud base. Returns: wlen_model : np.array Wavlength array of computed model, not binned to data [um] spectrum_model : np.array Computed emission spectrum [W/m2/micron] contr_em : Optional, np.ndarray Emission contribution function, relative contributions for each wavelength and pressure level. Only returns the contribution of the clear atmosphere component. .. py:function:: 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_object : object An instance of the pRT class, with optical properties as defined in the RunDefinition. parameters : dict 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_mode : bool 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_model : np.array Wavlength array of computed model, not binned to data [um] spectrum_model : np.array Computed transmission spectrum planet_radius**2/Rstar**2 contr-em : np.ndarray Optional, Emission contribution function, relative contributions for each wavelength and pressure level. .. py:function:: 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_object : object An instance of the pRT class, with optical properties as defined in the RunDefinition. parameters : dict 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_mode : bool 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_model : np.array Wavlength array of computed model, not binned to data [um] spectrum_model : np.array Computed transmission spectrum planet_radius**2/Rstar**2 contr-em : np.ndarray Optional, Emission contribution function, relative contributions for each wavelength and pressure level. .. py:function:: guillot_patchy_emission(prt_object, parameters, pt_plot_mode=False, amr=False) Deprecated, to be removed in future version .. py:function:: 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_object : object An instance of the pRT class, with optical properties as defined in the RunDefinition. parameters : dict 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] * nnodes : number 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_mode : bool 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_model : np.array Wavlength array of computed model, not binned to data [um] spectrum_model : np.array Computed transmission spectrum planet_radius**2/Rstar**2 contr-em : np.ndarray Optional, the emission contribution function, relative contributions for each wavelength and pressure level. .. py:function:: 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_object : object An instance of the pRT class, with optical properties as defined in the RunDefinition. parameters : dict 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_layers : number 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_mode : bool 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_model : np.array Wavlength array of computed model, not binned to data [um] spectrum_model : np.array Computed transmission spectrum planet_radius**2/Rstar**2 contr-em : np.ndarray Optional, the emission contribution function, relative contributions for each wavelength and pressure level. .. py:function:: 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_object : object An instance of the pRT class, with optical properties as defined in the RunDefinition. parameters : dict 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_mode : bool 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_model : np.array Wavlength array of computed model, not binned to data [um] spectrum_model : np.array Computed transmission spectrum planet_radius**2/Rstar**2 contr-em : np.ndarray Optional, the emission contribution function, relative contributions for each wavelength and pressure level. .. py:function:: 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_object : object An instance of the pRT class, with optical properties as defined in the RunDefinition. parameters : dict 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_mode : bool 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_model : np.array Wavlength array of computed model, not binned to data [um] spectrum_model : np.array Computed transmission spectrum planet_radius**2/Rstar**2 contr-em : np.ndarray Optional, the transmission contribution function, relative contributions for each wavelength and pressure level. .. py:function:: guillot_patchy_transmission(prt_object, parameters, pt_plot_mode=False, amr=False) Deprecated .. py:function:: 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_object : object An instance of the pRT class, with optical properties as defined in the RunDefinition. parameters : dict 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_mode : bool 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_model : np.array Wavlength array of computed model, not binned to data [um] spectrum_model : np.array Computed transmission spectrum planet_radius**2/Rstar**2 contr-em : np.ndarray Optional, the transmission contribution function, relative contributions for each wavelength and pressure level. Only the clear atmosphere contribution is returned. .. py:function:: 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_object : object An instance of the pRT class, with optical properties as defined in the RunDefinition. parameters : dict 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_mode : bool 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_model : np.array Wavlength array of computed model, not binned to data [um] spectrum_model : np.array Computed transmission spectrum planet_radius**2/Rstar**2 contr-em : np.ndarray Optional, the transmission contribution function, relative contributions for each wavelength and pressure level. Only the clear atmosphere contribution is returned. .. py:function:: madhu_seager_patchy_transmission(prt_object, parameters, pt_plot_mode=False, amr=False) Deprecated .. py:function:: 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_object : object An instance of the pRT class, with optical properties as defined in the RunDefinition. parameters : dict 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_mode : bool 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_model : np.array Wavlength array of computed model, not binned to data [um] spectrum_model : np.array Computed transmission spectrum planet_radius**2/Rstar**2 contr-em : np.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. .. py:function:: 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_object : object An instance of the pRT class, with optical properties as defined in the RunDefinition. parameters : dict 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_mode : bool 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_model : np.array Wavlength array of computed model, not binned to data [um] spectrum_model : np.array Computed transmission spectrum planet_radius**2/Rstar**2 contr-em : np.ndarray Optional, the emission contribution function, relative contributions for each wavelength and pressure level. .. py:function:: 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. .. py:function:: 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: press : numpy.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 .. py:function:: set_pglobal(press, parameters) Check to ensure that the global pressure array has the correct length. Updates PGLOBAL. Args: press : numpy.ndarray Pressure array from a prt_object. Used to set the min and max values of PGLOBAL parameters : dict Must include the 'pressure_simple' and 'pressure_scaling' parameters, used to determine the size of the high resolution grid. .. py:function:: 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 .. py:function:: 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_ .. py:function:: pglobal_check(press, shape, scaling) Check to ensure that the global pressure array has the correct length. Updates PGLOBAL. Args: press : numpy.ndarray Pressure array from a prt_object. Used to set the min and max values of PGLOBAL shape : int the shape of the pressure array if no amr is used scaling : The factor by which the pressure array resolution should be scaled.