Command line options ==================== Most of this section remains to be written. Basic options ------------- ``-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 `` [GB]: maximum memory that MCFOST can use (approx), default 8 Main options ------------ ``-img `` [microns]: computes image at specified wavelength ``-mol``: calculates molecular maps Coupling with other codes ------------------------- ``-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 `` : x,y,z values used for the Voronoi tesselation. ``-keep_particles `` (default: 0.99): fraction of SPH particles to keep for the Voronoi tesselation. File organisation ----------------- ``-seed ``: modifies seed for random number generator ; results stored in ``seed=XXX`` directory ``-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 ``: input directory for ProDiMo Options related to images ------------------------- ``-zoom ``: overrides value in parameter file ``-resol ``: 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 `` (default : 10 1) ``-planet_az `` [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 `` (default : 100) ``-tau_dark_zone_eq_th `` (default : 1500) ``-origin``: save origin of packets received the interest bin ``-rs (remove specie) `` ``-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 ``: changes the maximum temperature allowed for PAH (default: 2500) ``-ISM_heating``: includes heating by ISM radiation ``-chi_ISM ``: changes the chi of ISM radiation (default: 1) ``-no_internal_energy``: ignoring internal energy in Phantom dumps Disk structure -------------- ``-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 ``: forces cell subdivision elsewhere than at inner radius ``-3D``: 3D geometrical grid ``-warp`` : defined at reference radius ``-tilt``: [degrees] ``-cavity ``: 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 ``: add a puffed up inner rim to the disc, with an increased scale height by a factor and up to a radius r. The width over the scale goes back to normal is delta_r The updated scale height is .. math:: 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 ``: reads a fits file with the density (gas + dust + velocity, see section "Running a 3D model") ``-sigma_file or -sigma ``: reads a fits file with the surface density ``-correct_density ``: applies a correcting factir to the density between Rmin and Rmax. Can be used to generate rings or gaps. ``-gap ``: creates a Gaussian gap in the disc [depth is between 0 and 1, R and Sigma in au] ``-Seb_F ``: select the dust diffusion method frollowing Sebastian Fromang's prescriptions. 1 = gaussian, 2 = cst diffusion coeff ``-cutoff ``: 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 ``: 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. Stellar Properties ------------------- ``-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 `` adds limb darkening (including polarized limb darkening) on the stellar photosphere. Exemples of limb darkening files can be found in ``$MCFOST_UTILS/Stellar_Polarization``. ``-age `` (default: 3Myr). When using results from hydrodynamics simulations (e.g., SPH), mcfost will assume an age to determine the stellar luminosity and temperature from the mass. The age can be selected using:: Isochrones are found in ``$MCFOST_UTILS/Stellar_Polarization/Siess``. Dust properties --------------- ``-dust_prop``: computes opacity, albedo, asymmetry parameter, polarizability and saves results in ``data_dust`` ``-op `` [microns]: computes dust properties at specified wavelength and stops ``-aggregate `` ``-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 ``: 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 ``: 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. Options related to molecular emission ------------------------------------- ``-freeze-out ``: freeze-out molecules (abundance = 0) in regions below this temperature ``-freeze-out_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 ``: applies a factor to the gas temperature ``-chi_infall ``: v_infall/v_kepler ``-cylindrical_rotation``: forces Keplerian velocity of independent of z