Most of this section remains to be written.
-h, -help: displays the help message, with a summary of the main
options. Running mcfost withour any argument displays the same message.
-v : displays version number, and available updates
-setup : performs mcfost initial setup (downloads the data and parameter files)
-get_para: downloads the current version of the parameter file
-u: updates MCFOST to most recent version
-fu: forces MCFOST to update to the most recent version, even if there is
no new release available
-update_utils: updates MCFOST_UTILS to most recent version
-history: displays full MCFOST history since v2.12.9
-max_mem <value> [GB]: maximum memory that MCFOST can use (approx), default 8
-img <wavelength> [microns]: computes image at specified wavelength
-mol: calculates molecular maps
-prodimo: creates required files for ProDiMo.
-p2m: reads the results from ProDiMo.
-astrochem: creates required files for Astrochem.
-phamtom : reads a phantom dump file.
-gadget : reads a gadget-2 dump file.
-limits <limit-file> : x,y,z values used for the Voronoi tesselation.
-keep_particles <fraction> (default: 0.99): fraction of SPH particles to
keep for the Voronoi tesselation.
-seed <seed>: modifies seed for random number generator ; results stored in seed=XXX directory
-root_dir <root_dir>: results stored in root_dir directory
-no_backup : stops if directory data_XX already exists without attempting to backup existing directory
-prodimo_input_dir <dir>: input directory for ProDiMo
-zoom <zoom>: overrides value in parameter file
-resol <nx> <ny>: overrides value in parameter file
-PA: override value in parameter file
-only_scatt : ignore dust thermal emission
-casa : write an image ready for CASA
-nphot_img : overwrite the value in the parameter file
-rt: use ray-tracing method to compute images or SEDs (on by default)
-rt1 or -rt2: use ray-tracing method and force ray-tracing method
-no-rt: do not output the ray-tracing results
-mc: keep Monte-Carlo output in ray-tracing mode
-n_MC_bins <n_inclinations> <n_azimuth> (default : 10 1)
-planet_az <angle> [deg]: adjust the model azimuth so that the planet is at
desired azimuth in the map. 0 means the planet will be along the model x axis. Positive values from x axis to y axis.
Options related to temperature equilibrium
-no_T: skip temperature calculations, force ltemp to F
-diff_approx: enforce computation of T structure with diff approx.
-no_diff_approx: compute T structure with only MC method
-only_diff_approx: only compute the diffusion approx
-tau_dark_zone_obs <tau_dark_zone> (default : 100)
-tau_dark_zone_eq_th <tau_dark_zone> (default : 1500)
-origin: save origin of packets received the interest bin
-rs (remove specie) <specie_number> <Temperature>
-reemission_stats
-weight_emission: weight emission towards disk surface
-force_PAH_equilibrium: mainly for testing purposes
-force_PAH_out_equilibrium: mainly for testing purposes
-Tmax_PAH <T>: changes the maximum temperature allowed for PAH (default: 2500)
-ISM_heating: includes heating by ISM radiation
-chi_ISM <chi>: changes the chi of ISM radiation (default: 1)
-no_internal_energy: ignoring internal energy in Phantom dumps
-disk_struct: computes the density structure and stops:
gas_density.fits.gz and dust_density.fits.gz -> density map
grid.fits.gz -> radii and height in the grid
volume.fits.gz -> volume per cell at each radius
-r_subdivide <radius>: forces cell subdivision elsewhere
than at inner radius
-3D: 3D geometrical grid
-warp <h_warp>: defined at reference radius
-tilt: <angle> [degrees]
-cavity <h0> <r0> <flaring exponent>: carves a cavity in the the disc. Defines a surface, and empties the density above this surface.
-output_J: outputs the radiation field in each cell
-output_UV_field: output the UV radation field between 912 and 2000 Angströms in each cell. units: Habings
-puffed_up_rim <h_rim / h0> <r_rim> <delta_r>: add a puffed up inner rim to the disc, with an increased scale height by a factor <h rim / h0> and up to a radius r. The width over the scale goes back to normal is delta_r
The updated scale height is
h(r) = h_0(r) \times \left(1.0 + \frac{\frac{h_{rim}}{h_0} - 1.0}{\exp(\frac{r- r_{rim}}{\Delta r}) + 1.0} \right)
-density_file or -df <density_file>: reads a fits file with the density (gas + dust + velocity, see section "Running a 3D model")
-sigma_file or -sigma <surface_density_file>: reads a fits file with the surface density
-correct_density <factor> <Rmin> <Rmax>: applies a correcting factir to the density between Rmin and Rmax. Can be used to generate rings or gaps.
-gap <depth> <R> <sigma>: creates a Gaussian gap in the disc [depth is between 0 and 1, R and Sigma in au]
-Seb_F <number>: select the dust diffusion method frollowing Sebastian Fromang's prescriptions. 1 = gaussian, 2 = cst diffusion coeff
-cutoff <number>: upper limit of the grid [scale height] default = 7
-n_rad: overwrite value in parameter file
-nz: overwrite value in parameter file
-z_scaling_env <scaling_factor>: scale a spherical envelope along the z-axis
-column_density or -cd: outputs the column densities from any cell in 4 directions: to the star, to +z, to -z, and +x.
-spot <T_spot> <spot_surface_fraction> <i_spot> <phi_spot>: adds a cold or
hot spot on the photosphare. The spot surface fraction is defined between 0 and 1. The spot
inclination is defined between 0 and 180 degrees: 0 degree for a spot on
the pole and 90 degrees for a spot on the equator. The option currently only
works if the photosphere has no extra UV and is only available in MC mode so far.
If i is defined between 0 and 90 degrees, the spot is facing the
observer when using the central azimuthal bin.
-limb_darkening <ld_filename> adds limb darkening (including polarized limb
darkening) on the stellar photosphere. Exemples of limb darkening files can be found in
$MCFOST_UTILS/Stellar_Polarization.
-age <age> (default: 3Myr). When using results from hydrodynamics
simulations (e.g., SPH), mcfost will assume an age to determine the stellar
luminosity and temperature from the mass. The age can be selected using::
Isochrones are found in $MCFOST_UTILS/Stellar_Polarization/Siess.
-dust_prop: computes opacity, albedo, asymmetry parameter,
polarizability and saves results in data_dust
-op <wavelength> [microns]: computes dust properties at
specified wavelength and stops
-aggregate <GMM_input_file> <GMM_output_file>
-optical_depth_map, -od: generates a map of integrated optical depths from the centre of each cell.
4 directions are considered. In order: towards the star, +z, -z and +x.
Results are stored in optical_depth_map.fits.gz
-average_grain_size: computes average grain size in each cell,
weighted by their geometrical cross-section;
Results are stored in average_grain_size.fits.gz
-HG: uses an Heynyey-Greenstein function
-force_HG <g>: uses an Heynyey-Greenstein function and forces the g value
-isotropic: forces isotropic scattering
-no_scattering: forces albedo = 0
-qsca=qabs: forces albedo = 0.5
-phase-function <s11.fits>: uses a tabulated phase function (rt2 only)
-tau=1_surface: when computing an image, generates a fits file with the coordinates x,y,z of the tau=1 surface for each pixel. The dimension of the fits file is the same as the image fits file + an extra dimension with the 3 values x,y and z.
-freeze-out <T>: freeze-out molecules (abundance = 0) in regions below this temperature
-freeze-out_depletion <relative depletion>: between 0 and 1, depletion factor in the freeze-out region (default: 0)
-photo-dissociation: photo-dissociate molecules at high-UV (see Pinte et al 2018)
-photo-desorption: photo-desorb molecules at high-UV (see Pinte et al 2018)
-prodimo: generates a a fits file forProDiMo.fits.gz with the required information to run a thermo-chemical model with ProDiMo
-prodimo_fPAH: force a fPAH value for ProDiMo
-only_top: molecular emssion from the top half of the disk
-only_bottom: molecular emssion from the bottom half of the disk
-correct_Tgas <factor>: applies a factor to the gas temperature
-chi_infall <value>: v_infall/v_kepler
-cylindrical_rotation: forces Keplerian velocity of independent of z