Outputs from MCFOST =================== Outputs from SED mode calculations ---------------------------------- A calculation in SED mode will create a direcatory named ``data_th`` with the following files: - A copy of the input parameter file. A new line will be added at the end of this file, recording any command line options given in the call to MCFOST. - ``Temperature.fits.gz`` (and ``Temperature_DA.fits.gz`` if diffusion approximation is used) + additional temperature files of out-of-equilibrium grains are present - ``sed_rt.fits.gz``. This is the main output with the SED computed with a ray-tracing method. Ray-ytraced SEDs offer several advantages : they correspond to exact inclinations (instead of bins for ``sed_mc.fits.gz``) and converge almost equally fast at all inclinations. - ``sed_mc.fits.gz``. This file contains the SED computed with the MC method. It is mainly kept because it is small and can be used to double-check that the calculation went allright. Units for all SED files are W.m\ :sup:`-2`. The temperature map is in K, with values of 1K for regions where the temperature was not computed and is later estimated via the diffusion approximation (this occurs in extremely deep regions of disks). Output SED files typically are 4 dimensional. The dimensions are [wavelength, inclination, azimuth, contributions]. Dimensions may be of length 1; for instance typically the azimuth axis has only 1 value for the case of axisymmetric models. Corresponding wavelengths (in microns) are found in the second HDU of ``sed_rt.fits.gz``. An additional ``.sed_th.fits.gz`` is also created in the ``data_th`` directory. It records the SED produced by the Bjorkman & Wood algorithm during the calculation of the temperature. This file is generally noisy at wavelengths where the flux is low. It is mainly used for testing purposes. In particular, each re-emission takes place at the exact same location of the absorption, while in ``sed_mc.fits.gz`` and ``sed_rt.fits.gz``, the emissivity is assumed to be constant within a cell. The comparison of ``.sed_th.fits.gz`` and ``sed_mc.fits.gz`` can be useful to detect inadequate spatial resolution (ie cells that are too big to accurately sample the local emissivity). Outputs from Image calculations ------------------------------- - A copy of the input parameter file. A new line will be added at the end of this file, recording any command line options given in the call to MCFOST. - ``RT.fits.gz``: ray-traced output image - ``MC.fits.gz``: Monte-Carlo output image (if -mc option is used) Units for the images are W.m\ :sup:`-2`.pixel\ :sup:`-1`. These images have at least 3 dimensions, two spatial dimensions and one for inclination. Up to 5 dimensions may be present, in which case the 4th dimension is for the azimuthal viewing angle in case of a non-axisymmetric disk, and 5th dimension is the Stokes parameters for polarized imaging (I,Q,U and V) and different contributions if the contributions are separated (star alone, scattered light from the star, thermal emission, scattered light from the dust thermal emission). If the Stokes parameter option is turned on, the output is Stokes polarized intensities [I, Q, U, V] and *not* fractional polarization [I, Q/I, U/I, V/I]. That is to say, all the polarizations are written with the same dimensionality as intensities and units of W.m\ :sup:`-2`.pixel\ :sup:`-1`. .. note:: the -casa option makes the fits file compliant with casa and reduces the number of dimensions. Only the first inclination and azimuth are considered. Additional keywords are added for casa, units are changed to Jy/pixel. Outputs from Molecular Line calculations ---------------------------------------- - A copy of the input parameter file. A new line will be added at the end of this file, recording any command line options given in the call to MCFOST. - ``lines.fits.gz``: ray-traced data cube Units are in W.m\ :sup:`-2`.pixel\ :sup:`-1`. These images have 6 dimensions, 2 for spatial dimensions, 1 for velocity, 1 for the transition number, and 2 for the system inclination and azimuth. The files contains multiple HDUs. The 2nd HDU contains the continuum images, it has the same dimension as the main cube without the velocity. The 3rd and 4th HDUs contain the transition numbers and frequencies respectively. .. note:: the -casa option makes the fits file compliant with casa and reduces the number of dimensions. Only the first inclination and azimuth are considered. The fits file also only contains the main HDU in that case. Additional optional outputs --------------------------- Disk Density Files ^^^^^^^^^^^^^^^^^^ You can request an output of the computed disk density. This is done with the ``-disk_struct`` (or ``-output_density_grid``) command line option. This will output files in a ``data_disk`` directory: - ``gas_density.fits.gz`` [map of the gas density - in g/cm\ :sup:`3`] - ``dust_mass_density.fits.gz`` [map of the integrated dust density - in g/cm\ :sup:`3`] - ``dust_particule_density.fits.gz`` [map of the dust density - in part/cm\ :sup:`3`] - ``grain_sizes.fits.gz`` [grain size bins - in micron] - ``grid.fits.gz`` [map of the radii and height of the individual grid cells - in au] - ``volume.fits.gz`` [map of the volume of the individual grid cells - in au\ :sup:`3`] The various density files will have 3d arrays of dimension [``n_rad``, ``n_z`` or ``n_theta``, ``n_az``], where those parameters are as defined below in the parameter file geometry. The ``grid.fits.gz`` file will have those same dimensions for its first 3 axes, then the 4th axis will have dimension 2. The first plane in that axis will give the radius for each grid cell, the second will give the height. Dust Property Files ^^^^^^^^^^^^^^^^^^^ You can request an output of the computed dust propertis. Thies is done with the ``-dust_prop`` command line option. This will generate a ``data_dust`` directory that will contain the following output files (along with a copy of the parameter file): - ``albedo.fits.gz`` [table of the dust albedo] - ``g.fits.gz`` [table of the scattering phase function asymmetry parameter] - ``kappa.fits.gz`` [table of dust opacities - in cm\ :sup:`2`/g] - ``kappa\_grain.fits.gz`` [table of dust opacities as a function of grain size - in cm\ :sup:`2`/g] - ``lambda.fits.gz`` [table of wavelength at which the dust properties are computed - in micron] - ``phase\_function.fits.gz`` [table of scattering phase function from 0 to 180 degrees, versus wavelength] - ``polarizability.fits.gz`` [table of scattering polarizability from 0 to 180 degrees, versus wavelength] The ``lambda.fits.gz`` file also provides the wavelength array for an SED computation when ``lsed_complete`` is set to True (see below). If the dust properties are only needed at a specific wavelength (say 2.2 microns), the user can instead use the ``-op 2.2`` command line option. In this case, only the initialization sequence is performed, and the albedo and asymmetry parameter are given on screen at the end (as well as the total optical depth along the equatorial plane and along the viewing "inclination of interest" indicated in the parameter file). Note that these quantities are always provided in the normal run of MCFOST (for both SED and image calculations); this option merely stops the calculation after this stage. Note that a ``data_2.2`` directory is created containing only a copy of the parameter file. Optical depth maps ^^^^^^^^^^^^^^^^^^ Using the option ``-optical_depth_map`` or ``-od`` (in combination with ``-img``), mcfost will generate a fits file ``optical_depth_map.fits.gz`` of dimensions (n_rad, nz, n_az, 2) giving for the each cell the optical depth at the selected wavelentgh from the centre of the cell to r=0 and z=+infinity. When used in SED mode, the optical depth map will be computed at the wavelength closest to I band (e.g. 0.81 micron). Note that this option does not work yet when using a Voronoi mesh, the current implmentation only works for the rgular grids. Column density ^^^^^^^^^^^^^^ Option ``-cd`` generates a fits file ``column_density.fits.gz`` with the column density in each cells, in 4 directions: to the star, to z = + infinity, to z = - infinity, and to r = sqrt(x2 + y2) = infinity. tau=1 surface ^^^^^^^^^^^^^ Generates a fits file ``tau=1_surface.fits.gz`` giving for each pixel the coordinates x,y,z of the tau=1 surface. Tracking origin of packets ^^^^^^^^^^^^^^^^^^^^^^^^^^ Option ``-origin`` or ``-o`` creates a fits file ``origin.fits.gz``, which fraction of the energy received by the observer has been generated in that cell, i.e. it basically traces the 3D emitting regions for a given system orientation. Radiation field ^^^^^^^^^^^^^^^ Option ``-output_J`` generates a fits file ``J.fits`` with the radiation field in each cell and at each wavelength in W/m2. Option ``-output_UV_field`` generates a fits file ``UV_field.fits`` with, for each cell, the integrated radiation field between 912 and 200 angstroems (in Habing units). Files for ProDiMo ^^^^^^^^^^^^^^^^^ Option ``-prodimo`` will generate a single fits file ``forProDiMo.fits.gz`` which all the quantities required by ProDiMo to compute a thermo-chemical model. mcfost can then be used with the option ``-p2m`` to compute the corresponding data cube, based on the ProDiMo temperature structure and level populations. Files for Astochem ^^^^^^^^^^^^^^^^^^ Option ``-astrochem`` will generate all the files required to run a ``astrochem`` model.