Running a 3D model

MCFOST is completely 3D and can be used with any density structure. Interfaces for hydrodynamics codes can be built on demand if there are specific needs. There is also a default interface using FITS file to input MCFOST with any arbitrary density structure. This interface is likely to fulfill most of the needs.

It can be used with the command:

$ mcfost <parameter_file> -density_file <your_density_file.fits.gz> -3D (+ any other option)

Important

When using the -density_file or -sigma_file options, the number of zones must be set to 1 in mcfost

The density array in the FITS file must have 4 dimensions : density(1:n_rad, 1:nz, 1:n_az, 1:n_grains) (it then has n_rad x nz x n_az x n_grains elements).

The option -density_file also works in the 2D version of the code, ie without -3D. In that case the density file still requires 4 dimensions, but with n_az = 1 : density(1:n_rad, 1:nz, 1, 1:n_grains)

Note

the spatial grid is not currently passed to MCFOST in the FITS file. Instead, n_rad, nz and n_az must match the values provided in the parameter file. MCFOST will build the spatial grid from the parameter file (the grid can be cylindrical or spherical) and will assume the density is provided on this grid. The safest way to create the density file is then to first run:

$ mcfost <parameter_file> -density_struct

and read the file data_disk/grid.fits.gz to compute the density at the exact same points. As far as possible, you should try to match the MCFOST grid (ie, Rin, Rout, H₀, p) to the hydrodynamics simulations, this is will ensure a best use of the MCFOST cells.

Note

The value n_grains provided is the FITS file is independent of the one given in the parameter file on the other hand. MCFOST will assume that the n_grains 3D density structures provided in the FITS file are independent and will interpolate (in log of the grain size) between these densities for all the grain sizes requested in the parameter file. MCFOST does not extrapolate, ie all the grains smaller (larger) than the minimum (maximum) grain size provided in the FITS file will have the same spatial distribution as the minimum (maximum) grain size.

Important

If not provided, the gas is assumed to follow the density of the smallest grain size provided (you can however create an artificially small grain size for the gas if you wish).

There are 2 options to normalize the different spatial distribution of the grains relative to each other. These 2 options can be selected using the keyword read_n_a in the header of the 1st HDU of the FITS file.

If read_n_a is set to 0, the density structure does not need to be normalized. MCFOST will use the dust mass, grain size power law distribution and gas-to-dust mass ratio provided in the parameter file. In other words, the fits file is only used to pass the spatial distribution of each grain sizes and MCFOST will take care of all the required normalization.

If there are more than 1 grain size, the values of the n_grains grain sizes used in the FITS file in a second HDU with 1 dimension (NAXIS=1) : NAXIS1 = n_grains (unit : micron) : grain_sizes(1:n_grains). These grain sizes must be given in increasing order (and of course match the order of the data cube).

If read_n_a is set to 1, the relative density in each grain size bin needs passed to MCFOST and you must provide the grain size distribution integrated over the whole disk volume. This is done by using a 3st HDU where you pass an array of dimension (1:n_grains) providing the number of grains in each grain size bin : dn(a)/da

Note

the total normalization of the distribution is not required as MCFOST will use the total dust mass as set in the parameter file. The array n_a is only used to define the relative number of the grains of each size.

The gas density can be passed by setting the keyword read_gas_density to 1. In that case, an extra keyword gas_to_dust must also be passed to give the integrated gas to dust mass ratio. An extra HDU must also be passed, giving the gas density with 3 dimensions: gas_density(1:n_rad, 1:nz, 1:n_az). As for the dust density array, the array has 3 dimensions also in 2D, but with n_az=1. The total gas mass is set by the mcfost parameter file in any case. If the keyword read_gas_density is set to 0 or absent, mcfost will assume that the gas has the same spatial distribution as the smallest grains in the FITS file, and will use the gas-to-dust mass ratio provided in the parameter file.

Note

some parameters, such as read_gas_density are longer than 8 characters, which is the fits standard. They are however handled correctly by mcfost. In general, you can put a HIERARCH card in front of this parameter so that it respect fits standard. See for example Astopy’s documentation.

The gas velocity field, in Cartesian or cylindrical coordinates, can also be passed by setting read_gas_velocity to 1 (Cartesian coordinates) or 2 (cylindrical coordinates). The fits file must have an extra HDU with 4 dimensions: gas_velocity(1:n_rad, 1:nz, 1:n_az, 3). The last index correspond to v_x, v_y, v_z in Cartesian coordinates, or v_r, v_phi, v_z in cylindrical coordinates. The velocity is given in m/s.

Note

If the velocity is not passed via the fits interface, mcfost will assume that the velocity field is Keplerian (unless modified by command line options).

An alternative option -sigma_file works in a similar way with the vertical dimension and passes only the surface density. mcfost use the scale height and flaring index provided in the parameter file to reconstruct the 3D density structure.