Pyrat Bay:

Python Radiative Transfer in a Bayesian framework

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Author:

Patricio Cubillos and contributors (see Contributors)

Contact:

patricio.cubillos[at]oeaw.ac.at

Organizations:

Space Research Institute (IWF)

Web Site:

https://github.com/pcubillos/pyratbay

Date:

Feb 19, 2023

Features

Pyrat Bay is an efficient, user-friendly Python tool to compute radiative-transfer spectra, and fit exoplanet atmospheric properties. This package offers:

• Transmission or emission spectra of exoplanet transit or eclipses, respectively.

• Forward-model or retrieval calculations.

The radiative-transfer include opacity sources from:

• Line-by-line molecular absorption

• Collision-induced absorption

• Rayleigh scattering absorption

• Na and K alkali resonant lines

• Gray and Mie (soon) aerosol opacities

Bayesian (MCMC) posterior sampling of atmospheric parameters:

• Molecular abundances

• Temperature profile

• Pressure-radius

• Rayleigh and cloud properties

Contributors

• Patricio Cubillos (IWF, Austria) patricio.cubillos[at]oeaw.ac.at

• Jasmina Blecic (NYU, Abu Dhabi)

Documentation

• Getting Started
  • System Requirements
  • Install and Compile
  • Quick Example
  • Command-line Run
  • Interactive Run
• TLI Tutorial
  • Available Databases
  • Sample Configuration File
  • Databases
  • Partition Functions
  • Wavelength Boundaries
  • TLI Example
• Atmosphere Tutorial
  • Pressure Profile
  • Temperature Profiles
    • Isothemal profile
    • Guillot profile
    • Madhu profile
    • Temperature-profile Examples
  • Abundance Profiles
    • Uniform abundances
    • Thermochemical-equilibrium Abundances
    • Abundance-profile Examples
  • Altitude Profiles
    • Altitude-profile Examples
• Spectrum Tutorial
  • Sample Configuration File
  • Observing Geometry
  • Atmospheric Model
  • Spectrum Sampling
  • Voigt Profiles
  • System Parameters
    • Hill radius
    • Stellar spectrum
    • Radius Ratio
  • Line-by-line Opacities
  • Cross-section Opacities
  • Radius-profile Models
  • Alkali Opacity Models
  • Rayleigh Opacity Models
  • Cloud Opacity Models
  • Patchy Cloud/Hazes
  • Temperature Models
  • Abundances Scaling
  • Stellar Spectrum
  • Filter Pass-bands
  • Observed Data
  • Other Configuration Parameters
    • Number of CPUs
    • Verbosity
    • Log File
    • Optical-depth Cutoff
    • Plane-parallel Hemispheric Integration
  • Examples
• Opacity-grid Tutorial
  • Sample Configuration File
  • Opacity Table as Input/output
  • Examples
• MCMC Tutorial
  • Sample Configuration File
  • Observed Data
  • Retrieval Models and Parameters
  • Parameter Priors
  • Retrieval Setup
    • MCMC Retrieval
  • Examples
• Cookbooks
• API
  • pyratbay
    • Pyrat
    • run()
  • pyratbay.constants
    • h
    • k
    • c
    • G
    • sigma
    • eV
    • A
    • nm
    • um
    • mm
    • cm
    • m
    • km
    • au
    • pc
    • rearth
    • rjup
    • rsun
    • barye
    • mbar
    • pascal
    • bar
    • atm
    • gram
    • kg
    • mearth
    • mjup
    • msun
    • amu
    • me
    • kelvin
    • sec
    • min
    • hour
    • day
    • amagat
    • e
    • percent
    • ppt
    • ppm
    • none
    • C1
    • C2
    • C3
    • ROOT
    • tlireclen
    • dreclen
    • ireclen
    • sreclen
    • dbases
    • rmodes
    • transmission_rt
    • emission_rt
    • rt_paths
    • retflags
    • tmodels
    • chemmodels
    • radmodels
    • molmodels
    • amodels
    • rmodels
    • cmodels
  • pyratbay.io
    • save_pyrat()
    • load_pyrat()
    • write_atm()
    • read_atm()
    • write_spectrum()
    • read_spectrum()
    • write_opacity()
    • read_opacity()
    • write_pf()
    • read_pf()
    • write_cs()
    • read_cs()
    • read_pt()
    • read_observations()
    • read_atomic()
    • read_molecs()
    • read_isotopes()
    • import_xs()
    • import_tea()
    • export_pandexo()
  • pyratbay.tools
    • log_error()
    • cd()
    • tmp_reset()
    • binsearch()
    • divisors()
    • unpack()
    • u()
    • get_param()
    • ifirst()
    • ilast()
    • isfile()
    • file_exists()
    • path()
    • Formatted_Write
    • Timer
    • get_exomol_mol()
    • cia_hitran()
    • cia_borysow()
    • radius_to_depth()
    • depth_to_radius()
    • ignore_system_exit()
    • Namespace
    • parse()
    • parse_str()
    • parse_int()
    • parse_float()
    • parse_array()
  • pyratbay.opacity
    • make_tli()
  • pyratbay.opacity.linelist
    • Hitran
    • Exomol
    • Repack
    • Pands
    • Tioschwenke
    • Voplez
    • Vald
  • pyratbay.opacity.partitions
    • get_tips_molname()
    • tips()
    • exomol()
    • kurucz()
  • pyratbay.opacity.broadening
    • Lorentz
    • Gauss
    • Voigt
    • doppler_hwhm()
    • lorentz_hwhm()
    • min_widths()
    • max_widths()
  • pyratbay.plots
    • alphatize()
    • spectrum()
    • contribution()
    • temperature()
    • abundance()
    • default_colors
  • pyratbay.spectrum
    • blackbody_wn()
    • blackbody_wn_2D()
    • bbflux()
    • read_kurucz()
    • PassBand
    • Tophat
    • tophat()
    • resample()
    • band_integrate()
    • contribution_function()
    • transmittance()
    • band_cf()
    • convective_flux()
    • radiative_equilibrium()
  • pyratbay.atmosphere
    • pressure()
    • temperature()
    • chemistry()
    • uniform()
    • abundance()
    • hydro_g()
    • hydro_m()
    • rhill()
    • stoich()
    • mean_weight()
    • ideal_gas_density()
    • equilibrium_temp()
    • transit_path()
    • temperature_posterior()
    • qcapcheck()
    • balance()
    • ratio()
    • qscale()
  • pyratbay.atmosphere.tmodels
    • Isothermal
    • Guillot
    • Guillot
    • Madhu
    • get_model()
  • pyratbay.atmosphere.clouds
    • CCSgray
    • Deck
    • get_model()
  • pyratbay.atmosphere.rayleigh
    • Dalgarno
    • Lecavelier
    • get_model()
  • pyratbay.atmosphere.alkali
    • SodiumVdW
    • PotassiumVdW
    • get_model()
  • pyratbay.pyrat.read_atm
  • pyratbay.pyrat.crosssec
  • pyratbay.pyrat.clouds
  • pyratbay.pyrat.rayleigh
  • pyratbay.pyrat.alkali
  • pyratbay.pyrat.optical_depth
  • pyratbay.pyrat.spectrum
    • spectrum()
    • modulation()
    • intensity()
    • flux()
    • two_stream()
• Units
• References
• Contributing
  • Raising Issues
  • Programming Style
  • Pull Requests
• License

Be Kind

If you found Pyrat Bay useful for your research, please cite this article:

Cubillos & Blecic (2021): The Pyrat Bay Framework for Exoplanet Atmospheric Modeling: A Population Study of Hubble/WFC3 Transmission Spectra, MNRAS, 505, 2675.

Please prefer to channel your feedback or inquiries through the Github issue tracker: https://github.com/pcubillos/pyratbay, or alternatively through this email: patricio.cubillos[at]oeaw.ac.at.

Pyrat Bay is open-source software under the GNU GPL v2 license (see License) and is compatible with Python>=3.6.