astroMUGS in details

A detailed description of all classes, methods, and modules.

Modeling

• The Grid
  • Overview
  • Setting up a spherical grid
  • Setting up a chemistry grid
  • API Reference
• The Disk model
  • Overview
  • Key concepts
    • Surface density and settling
    • Vertical temperature structure
  • API Reference
    • Disk
      • Disk.scaleheight()
      • Disk.surfacedensity()
      • Disk.omega2()
      • Disk.temp_mid()
      • Disk.temp_atmos()
      • Disk.temp_altitude()
      • Disk.verticaldensity_gauss()
      • Disk.density()
      • Disk.numberdensity()
      • Disk.viscous_accretion_heating()
      • Disk.surfacedensity_d()
      • Disk.scaleheight_d()
      • Disk.density_d()
      • Disk.numberdensity_d()
      • Disk.numberdensity_d_single()
      • Disk.q_ext()
      • Disk.av_z()
      • Disk.avz_ism()
• The Model class
  • Overview
  • Writing Nautilus input files
  • Converting Nautilus output to RADMC3D
  • API Reference
• Input files
  • Custom input file format

Radiative transfer

• Radiative transfer simulations
  • Write dust continuum radiative transfer RADMC3D input files

Chemistry

• Gas-grain simulations
  • Write NAUTILUS input files
    • Step 1 — Add a dust model
    • Step 2 — Define the radial grid
    • Step 3 — Set the vertical chemistry grid
      • set_chemdisk_grid — scale-height based (recommended for disk models)
      • set_chem_grid — altitude based (envelope or custom geometries)
    • Step 4 — Write Nautilus input files
      • Key arguments
  • Best practices
    • Stay in the Nautilus safe zone
  • Read NAUTILUS output binaries
    • Loading chemistry results
    • Disk mode: accessing data per radius
    • Working with the abundances DataArray (xarray)
    • Plotting a vertical abundance profile
    • Single-run mode (0-D / single column)
    • Monitoring a running job
• RADMC3D – Nautilus coupling
  • Overview
  • Coordinate conversion
  • Converting RADMC-3D to Nautilus input files
    • Density coupling
    • Temperature coupling
    • UV extinction coupling
  • Converting Nautilus abundances back to RADMC-3D
  • API Reference
    • moving_average()
    • dust_density()
    • dust_temperature_disk()
    • dust_temperature_single_disk()
    • dust_temperature()
    • dust_temperature_single()
    • local_field()
    • avz_disk()
    • av_z()
    • to_spherical()

API Reference

• API Reference
  • Pipeline
    • Interface
      • Interface.add_chemical_path()
      • Interface.add_thermal_path()
      • Interface.add_star()
      • Interface.add_isrf()
      • Interface.add_disk()
      • Interface.add_internalheating()
      • Interface.add_chemdisk()
      • Interface.add_envelope()
      • Interface.add_chemistry()
      • Interface.convert_nautilus2radmc()
      • Interface.run_chemistry()
      • Interface.run_chemistry_custompath()
      • Interface.run_continuum()
      • Interface.run_image_radmc3d()
      • Interface.run_line()
      • Interface.run_localfield()
      • Interface.run_localfield_radmc3d()
      • Interface.run_thermal_radmc3d()
      • Interface.write_continuum()
      • Interface.write_line()
      • Interface.write_nautilus()
    • Pipeline
      • Pipeline.params
      • Pipeline.thermalparams
      • Pipeline.thermalpath
      • Pipeline.chempath
      • Pipeline.radmc3d_cmd
      • Pipeline.grid
      • Pipeline.nautilus
      • Pipeline.Ta
      • Pipeline.run_continuum()
      • Pipeline.run_line()
      • Pipeline.convert_nautilus2radmc()
      • Pipeline.run_localfield()
      • Pipeline.run_thermal_radmc3d()
      • Pipeline.run_chemistry()
      • Pipeline.run_chemistry_custompath()
      • Pipeline.run_localfield_radmc3d()
      • Pipeline.run_image_radmc3d()
      • Pipeline.write_continuum()
      • Pipeline.write_line()
      • Pipeline.write_nautilus()
    • Grid
      • Grid.params
      • Grid.wave
      • Grid.density
      • Grid.dustdensity
      • Grid.gasdensity_chem
      • Grid.dustdensity_chem
      • Grid.dustdensity_single_chem
      • Grid.hg_chem
      • Grid.tgas_chem
      • Grid.temperature
      • Grid.localfield
      • Grid.avz
      • Grid.stars
      • Grid.isrf
      • Grid.dust
      • Grid.accretionheating
      • Grid.chemradii
      • Grid.chemparam
      • Grid.chemmodel
      • Grid.add_star()
      • Grid.add_isrf()
      • Grid.add_temperature()
      • Grid.add_localfield()
      • Grid.add_density()
      • Grid.add_dustdensity()
      • Grid.add_dustdensity_chem()
      • Grid.add_dustdensity_single_chem()
      • Grid.add_gasdensity_chem()
      • Grid.add_gastemperature_chem()
      • Grid.add_hg_chem()
      • Grid.add_avz()
      • Grid.add_dust()
      • Grid.add_accretionheating()
      • Grid.add_existingchemradii()
      • Grid.add_existingchemparam()
      • Grid.add_existingchemmodel()
      • Grid.set_cartesian_grid()
      • Grid.set_spherical_grid()
      • Grid.set_chemdisk_grid()
      • Grid.set_chem_grid()
      • Grid.set_wavelength_grid()
      • Grid.set_mcmonowavelength_grid()
  • Modeling
    • astromugs.modeling.Disk
      • Disk
        • Disk.__init__()
    • astromugs.modeling.Star
      • Star
        • Star.__init__()
    • astromugs.modeling.Envelope
      • Envelope
        • Envelope.__init__()
  • Nautilus interface
    • astromugs.nautilus.coupling
    • astromugs.nautilus.write
    • astromugs.nautilus.read
  • Dust models
    • astromugs.dust
      • astromugs.dust.CustomDistrib
        • CustomDistrib
          • CustomDistrib.__init__()
      • astromugs.dust.MRNDistrib
        • MRNDistrib
          • MRNDistrib.__init__()
  • Plotting
    • astromugs.plotting
      • astromugs.plotting.plot
  • Utilities
    • astromugs.utils
      • astromugs.utils.custom
      • astromugs.utils.struct
      • astromugs.utils.thermal