RADMC-3D Version 2.0, an astrophysics radiative transfer tool

• Introduction
  • What is RADMC-3D?
  • Capabilities
  • Version tracker
  • Copyright
  • Contributing authors
  • Disclaimer
• Quickstarting with RADMC-3D
• Overview of the RADMC-3D package
  • Introduction
  • Requirements
  • Contents of the RADMC-3D package
    • RADMC-3D package as a .zip archive
    • RADMC-3D package from the github repository
    • Contents of the package
  • Units: RADMC-3D uses CGS units
• Installation of RADMC-3D
  • Compiling the code with ‘make’
  • The install.perl script
  • What to do if this all does not work?
  • Installing the simple Python analysis tools
    • How to install and use the python/radmc3d_tools/
    • How to install and use the python/radmc3dPy library
  • Making special-purpose modified versions of RADMC-3D (optional)
• Basic structure and functionality
  • Basic dataflow
  • Radiative processes
  • Coordinate systems
  • The spatial grid
  • Computations that RADMC-3D can perform
  • How a model is set up and computed: a rough overview
  • Organization of model directories
  • Running the example models
• Dust continuum radiative transfer
  • The thermal Monte Carlo simulation: computing the dust temperature
    • Modified Random Walk method for high optical depths
  • Making SEDs, spectra, images for dust continuum
  • OpenMP parallelized Monte Carlo
  • Overview of input data for dust radiative transfer
  • Special-purpose feature: Computing the local radiation field
  • More about scattering of photons off dust grains
    • Five modes of treating scattering
    • Scattering phase functions
  • Scattering of photons in the Thermal Monte Carlo run
  • Scattering of photons in the Monochromatic Monte Carlo run
    • Scattered light in images and spectra: The ‘Scattering Monte Carlo’ computation
    • Single-scattering vs. multiple-scattering
    • Simplified single-scattering mode (spherical coordinates)
    • Warning when using an-isotropic scattering
    • For experts: Some more background on scattering
  • Polarization, Stokes vectors and full phase-functions
    • Definitions and conventions for Stokes vectors
    • Our conventions compared to other literature
    • Defining orientation for non-observed radiation
    • Polarized scattering off dust particles: general formalism
    • Polarized scattering off dust particles: randomly oriented particles
    • Scattering and axially symmetric models
  • More about photon packages in the Monte Carlo simulations
  • Polarized emission and absorption by aligned grains
    • Basics
    • Implementation in RADMC-3D
    • Consistency with other radiative processes
    • Input files for RADMC-3D for aligned grains
    • Effect of aligned grains on the scattering
  • Grain size distributions
    • Quick summary of how to implement grain sizes
    • Method 1: Size distribution in the opacity file (faster)
    • Method 2: Size distribution in the density file (better)
    • The mathematics of grain size distributions
• Line radiative transfer
  • Quick start for adding line transfer to images and spectra
  • Some definitions for line transfer
  • Line transfer modes and how to activate the line transfer
    • Two different atomic/molecular data file types
    • The different line modes (the lines_mode parameter)
  • The various input files for line transfer
    • INPUT: The line transfer entries in the radmc3d.inp file
    • INPUT: The line.inp file
    • INPUT: Molecular/atomic data: The molecule_XXX.inp file(s)
    • INPUT: Molecular/atomic data: The linelist_XXX.inp file(s)
    • INPUT: The number density of each molecular species
    • INPUT: The gas temperature
    • INPUT: The velocity field
    • INPUT: The local microturbulent broadening (optional)
    • INPUT for LTE line transfer: The partition function (optional)
    • INPUT: The number density of collision partners (for non-LTE transfer)
  • Making images and spectra with line transfer
    • Speed versus realism of rendering of line images/spectra
    • Line emission scattered off dust grains
  • Non-LTE Transfer: The Large Velocity Gradient (LVG) + Escape Probability (EscProb) method
  • Non-LTE Transfer: The optically thin line assumption method
  • Non-LTE Transfer: Full non-local modes (FUTURE)
  • Non-LTE Transfer: Inspecting the level populations
  • Non-LTE Transfer: Reading the level populations from file
  • What can go wrong with line transfer?
  • Preventing doppler jumps: The ‘doppler catching method’
  • Background information: Calculation and storage of level populations
  • In case it is necessary: On-the-fly calculation of populations
  • For experts: Selecting a subset of lines and levels ‘manually’
• Making images and spectra
  • Basics of image making with RADMC-3D
  • Making multi-wavelength images
  • Making spectra
    • What is ‘in the beam’ when the spectrum is made?
    • Can one specify more realistic ‘beams’?
  • Specifying custom-made sets of wavelength points for the camera
    • Using lambdarange and (optionally) nlam
    • Using allwl
    • Using loadcolor
    • Using loadlambda
    • Using iline, imolspec etc (for when lines are included)
  • Heads-up: In reality wavelength are actually wavelength bands
    • Using channel-integrated intensities to improve line channel map quality
  • The issue of flux conservation: recursive sub-pixeling
    • The problem of flux conservation in images
    • The solution: recursive sub-pixeling
    • A danger with recursive sub-pixeling
    • Recursive sub-pixeling in spherical coordinates
    • How can I find out which pixels RADMC-3D is recursively refining?
    • Alternative to recursive sub-pixeling
  • Stars in the images and spectra
  • Second order ray-tracing (Important information!)
    • Second order integration in spherical coordinates: a subtle issue
  • Circular images
  • Visualizing the \(\tau=1\) surface
  • Maps of optical depth \(\tau\)
  • For public outreach work: local observers inside the model
  • Multiple vantage points: the ‘Movie’ mode
• More information about the gridding
  • Regular grids
  • Separable grid refinement in spherical coordinates (important!)
  • Oct-tree Adaptive Mesh Refinement
  • Layered Adaptive Mesh Refinement
    • On the ‘successively regular’ kind of data storage, and its slight redundancy
  • Unstructured grids
  • 1-D Plane-parallel models
    • Making a spectrum of the 1-D plane-parallel atmosphere
    • In 1-D plane-parallel: no star, but incident parallel flux beams
    • Similarity and difference between 1-D spherical and 1-D plane-parallel
  • Thermal boundaries in Cartesian coordinates
• More information about the treatment of stars
  • Stars treated as point sources
  • Stars treated as spheres
  • Distributions of zillions of stars
  • The interstellar radiation field: external source of energy
    • Role of the external radiation field in Monte Carlo simulations
    • Role of the external radiation field in images and spectra
  • Internal heat source
    • Slow performance of RADMC-3D with heat source
• Modifying RADMC-3D: Internal setup and user-specified radiative processes
  • Setting up a model inside of RADMC-3D
  • The pre-defined subroutines of the userdef_module.f90
  • Some caveats and advantages of internal model setup
  • Using the userdef module to compute integrals of \(J_\nu\)
  • Some tips and tricks for programming user-defined subroutines
  • Creating your own emission and absorption processes
• Python analysis tool set
  • The simpleread.py library
  • The radmc3dPy library
  • Model creation from within radmc3dPy
  • Diagnostic tools in radmc3dPy
    • Read the amr_grid.inp file
    • Read all the spatial data
    • Read the image.out file
    • Read the spectrum.out file
• Analysis tools inside of radmc3d
  • Making a regularly-spaced datacube (‘subbox’) of AMR-based models
    • Creating a subbox
    • Format of the subbox output files
    • Using the radmc3d_tools to read the subbox data
  • Alternative to subbox: arbitrary sampling of AMR-based models
• Visualization with VTK tools (e.g. Paraview or VisIt)
• Tips, tricks and problem hunting
  • Tips and tricks
  • Bug hunting
  • Some tips for avoiding troubles and for making good models
  • Careful: Things that might go wrong
  • Common technical problems and how to fix them
• Main input and output files of RADMC-3D
  • INPUT: radmc3d.inp
  • INPUT (required): amr_grid.inp
    • Regular grid
    • Oct-tree-style AMR grid
    • Layer-style AMR grid
  • INPUT (required for dust transfer): dust_density.inp
    • Example: dust_density.inp for a regular grid
    • Example: dust_density.inp for an oct-tree refined grid
    • Example: dust_density.inp for a layer-style refined grid
  • INPUT/OUTPUT: dust_temperature.dat
  • INPUT (mostly required): stars.inp
  • INPUT (optional): stellarsrc_templates.inp
  • INPUT (optional): stellarsrc_density.inp
  • INPUT (optional): external_source.inp
  • INPUT (optional): heatsource.inp
  • INPUT (required): wavelength_micron.inp
  • INPUT (optional): camera_wavelength_micron.inp
  • INPUT (required for dust transfer): dustopac.inp and dustkappa_*.inp or dustkapscatmat_*.inp or dust_optnk_*.inp
    • The dustopac.inp file
    • The dustkappa_*.inp files
    • The dustkapscatmat_*.inp files
  • OUTPUT: spectrum.out
  • OUTPUT: image.out or image_****.out
  • INPUT: (minor input files)
    • The color_inus.inp file (required with comm-line option ‘loadcolor’)
    • INPUT: aperture_info.inp
  • For developers: some details on the internal workings
• Binary I/O files
  • Overview
  • How to switch to binary (or back to ascii)
  • Binary I/O file format of RADMC-3D
• Command-line options
  • Main commands
  • Additional arguments: general
  • Switching on/off of radiation processes
• Which options are mutually incompatible?
  • Coordinate systems
  • Scattering off dust grains
  • Local observer mode
• Acquiring opacities from the WWW
• Version tracker: Development history

Indices and tables

• Index

• Module Index

• Search Page