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RADMC3D setup

This is a brief overview of some of the options that are set for RADMC-3D. For most DiskJockey use, the user need only be concerned about the gridding setup. However, some of the files written out to interface with RADMC-3D are documented here for reference.

Gridding

Most models are specified (mathematically) as 2D axisymmetric in cylindrical coordinates. RADMC-3D takes files in spherical coordinates, and so this conversion is done in model.jl as the model is written out.

Generally, the grid cells are logarithmically spaced in radius. The elevation (theta) cells are logarithmically spaced in theta, with cells clustered more denesly near the midplane than at the poles. Because of the axisymmetry, there is only one phi (azimuth) cell.

Although RADMC-3D has the ability to determine dust temperatures through radiative Monte Carlo, we set the gas temperatures directly though a simple radial temperature profile.

Then, the user also chooses the number of pixels npix for the resulting image to have. A good rule of thumb is that pixels need to be roughly 5-10x smaller than the resolution of the interferometric observations.

Files required for line transfer and what they are

  • lines.inp: control file for line transfer
  • molecule_co.inp contains properties of atom or molecule
  • numberdens_co.inp number density of molecule in units of cm^{-3}
  • gas_temperature.inp gas temperature at each grid cell

radmc.inp

tgas_eq_tdust=0 #this means we will specify the gas temperature at each grid cell, rather than setting it equal to the dust temperature.

lines.inp

Format styles

1 #format style 1 (may be 2)
1
co    leiden    0    0

This means that we will only be using the CO molecule. All of the information about this molecule is stored in the file molecule_co.inp. This is read from the Leiden database. Basically it provides all of the quantum information about the energy levels.

numberdens_XXX.inp

The number density of each species per cubic centimeter.

gas_temperature.inp

Specifies the gas temperature at each cell.

gas_velocity.inp

Three numbers at each grid point, which are the components of velocity along each direction. All components have units of cm/s.

microturbulence.inp

We can also specify a microturbulent broadening for each cell.

partitionfunction_XXX.inp

This can be specified for CO or other species. Otherwise RADMC3D will calculate the partition function itself using the molecular data file.

amr_grid.inp

We can use different coordinate systems here.

**coordsystem**:
< 100: cartesian
100<= - <200: spherical
200<= - <300: cylindrical

If we want to make a spherical grid, using 2D symmetry, we can specify that we wish one dimension to be non-active.

The files that need to be generated by our package are

  • amr_grid.inp: location of grid cells
  • microturbulence.inp: microturbulence at each cell
  • gas_velocity.inp: three component velocity vector at each cell
  • numberdens_co.inp: the number density of the CO molecule at each cell

All of the other files can be pre-generated or lifted from some database.