Monte Carlo Radiative Transfer
This page explains the options for Monte Carlo radiative transfer (MCRT) simulations.
General MCRT Parameters
The following parameters are important MCRT parameters:
n_photons– Actual number of photon packets used. [Default value: 1]output_photons– Flag to output escaped and absorbed photon packets. [Default value: true]photon_file– Output a separate photon file with this base name, e.g. “photons”. [Optional]output_n_scat– Flag to output the number of scattering events for photon packets. [Default value: false]output_collisions– Flag to output collisional excitation data for photons and cameras. [Default value: false]output_source_position– Flag to output the emission position for photon packets. [Default value: false]
Line Parameters
The following parameters are related to line specifications:
line– Name of the line to be modeled. [Default value: Lyman-alpha | Other options: Balmer-alpha, Balmer-beta, Balmer-gamma, Balmer-delta, Balmer-epsilon, Paschen-alpha, Paschen-beta, Brackett-alpha, CIII-1907-1909, CIV-1548-1550, NII-6550, NII-6585, NIII-1747-1749, NIV-1486, OI-6302, OI-6366, OII-3727-3730, OIII-1661-1666, OIII-4364, OIII-4933, OIII-4960, OIII-5008, NeIII-3969, MgII-2796-2803, SiII-1190-1193, SiII-1260, SiII-1304, SiII-1527, SiIII-1206, SiIV-1394-1403, SII-6718, SII-6733]dust_model– Dust model for the line radiative transfer. [Options: SMC, MW, LAURSEN_SMC, filename]kappa_dust– Dust opacity at the wavelength of the line. [Default value: Based on dust_model and line | Units: cm^2/g of dust]sigma_dust– Dust cross section at the wavelength of the line. [Default value: Based on dust_model and line | Units: cm^2/Z/hydrogen atom]albedo– Dust scattering albedo defined as \(A = k_\text{scat} / (k_\text{abs} + k_\text{scat})\). [Default value: Based on dust_model and line | Valid range: 0 < albedo < 1]g_dust– Anisotropy parameter \(\langle \mu \rangle\) for dust scattering. [Default value: Based on dust_model and line | Valid range: -1 < g_dust < 1]f_ion– Survival fraction of dust in \({\rm H\,{\small II}}\) regions. [Default value: 1 | Valid range: 0 < f_ion < 1]T_sputter– Thermal sputtering temperature cutoff, such that no dust exists within gas hotter than this value. [Default value: 1e6 | Units: K]p_dest– Line destruction probability between absorption and re-emission. [Default value: 0 | Valid range: 0 < p_dest < 1]
Resonance Line Parameters
The following parameters are related to resonance lines:
recoil– Include recoil induced Doppler shifting with line scattering. [Default value: true]x_crit– Constant critical frequency for core-skipping. [Default value: 0 | Valid range: x_crit > 0]dynamical_core_skipping– Non-local core-skipping for resonance lines. [Default value: false]n_exp_atau– Healpix exponent for the non-local \(a \tau_0\) core-skipping estimates, resulting in \(12 \times 4^{n_\text{exp,atau}}\) directions. [Default value: 0 | Valid range: n_exp_atau >= 0]n_side_atau– Healpix number of base pixel subdivisions for the non-local \(a \tau_0\) core-skipping estimates, resulting in \(12 \times n_\text{side,atau}^2\) directions. [Overrides n_exp_atau | Default value: 1 | Valid range: n_side_atau >= 1]
Exit Parameters
The following parameters are related to exit options:
doppler_frequency– Output frequency in units of Doppler widths, otherwise as a velocity offset from line center (in units of km/s). [Default value: false]T_exit– Exit temperature for standardized Doppler frequency. [Default value: 1e4 | Units: K]v_exit– Exit velocity for shifted observer frames. [Default value: (0,0,0) | Units: cm/s]exit_wrt_com– Exit with respect to the center of mass velocity frame. [Default value: false]
Note
In what follows the units of “freq” refer to km/s unless using doppler_frequency.
Radiation Source Parameters
The following parameters are related to line radiative transfer options:
recombinations– Include recombination emission with luminosity \(\mathcal{L}_\text{rec} = h \nu_0 \int \alpha_\text{B,eff}(T) n_e n_\text{HII} \text{d}V\). [Default value: false]collisions– Include collisional excitation emission with luminosity for Lyα of \(\mathcal{L}_\text{col} = h \nu_0 \int q_\text{col}(T) n_e n_\text{HI} \text{d}V\). Note: This flag also works for all implemented hydrogen lines and many collisionally excited metal lines. [Default value: false]continuum– Include stellar continuum emission around the line. [Default value: false]continuum_range– Continuum velocity offset range for frequency sampling. [Default value: (-2000,2000) | Units: km/s]j_exp– Luminosity boosting exponent for power-law emission biasing, i.e. probabilities are rescaled according to \(\propto \mathcal{L}_\text{cell}^{j_\text{exp}}\) such that \(j_\text{exp} < 1\) can better sample lower emissivity regions. [Default value: 1 | Valid range: 0 < j_exp < 1]emission_n_min– Minimum number density of emitting cells. [Default value: 0 | Units: cm^-3]emission_n_max– Maximum number density of emitting cells. [Default value: infinity | Units: cm^-3]emission_ne_min– Minimum electron number density of emitting cells. [Default value: 0 | Units: cm^-3]emission_ne_max– Maximum electron number density of emitting cells. [Default value: infinity | Units: cm^-3]point– Point source position in [0 0 0] format. [Optional | Units: cm]x_point– Point source \(x\) position. [Optional | Units: cm]y_point– Point source \(y\) position. [Optional | Units: cm]z_point– Point source \(z\) position. [Optional | Units: cm]L_point– Point source luminosity. [Default value: 1 | Units: erg/s]r_shell– Shell source radius. [Optional | Units: cm]L_shell– Shell source luminosity. [Default value: 1 | Units: erg/s]
Camera Parameters
The following parameters are related to cameras options:
n_bins– Number of frequency bins. [Default value: 100]n_slit_bins– Number of frequency bins for slits. [Default value: n_bins]n_cube_bins– Number of frequency bins for data cubes. [Default value: n_bins]n_radial_cube_bins– Number of frequency bins for radial data cubes. [Default value: n_bins]freq_range– Frequency extrema in [-1000 1000] format. Note: Similar setup forslit_freq_range,cube_freq_range, andradial_cube_freq_range. [Default value: (-1000,1000) | Units: freq]freq_min– Frequency range minimum. Note: Similar setup forslit_freq_min,cube_freq_min, andradial_cube_freq_min. [Default value: -1000 | Units: freq]freq_max– Frequency range maximum. Note: Similar setup forslit_freq_max,cube_freq_max, andradial_cube_freq_max. [Default value: 1000 | Units: freq]output_fluxes– Output spectral fluxes. [Default value: true | Dimensions: (n_cameras, n_bins) | Output units: erg/s/cm^2/angstrom]output_images– Output surface brightness images. [Default value: true | Dimensions: (n_cameras, nx_pixels, ny_pixels) | Output units: erg/s/cm^2/arcsec^2]output_slits– Output spectral slits. [Default value: false | Dimensions: (n_cameras, n_slit_pixels, n_slit_bins) | Output units: erg/s/cm^2/arcsec^2/angstrom]output_cubes– Output spectral data cubes. [Default value: false | Dimensions: (n_cameras, nx_cube_pixels, ny_cube_pixels, n_cube_bins) | Output units: erg/s/cm^2/arcsec^2/angstrom]output_images2– Output statistical moment images, e.g. to estimate convergence statistics as the relative error is approximately \(\sqrt{\text{images2}} / \text{images}\). [Default value: false | Dimensions: (n_cameras, nx_pixels, ny_pixels) | Output units: erg^2/s^2/cm^4/arcsec^4]output_radial_images– Output radial surface brightness images. [Default value: false | Dimensions: (n_cameras, n_radial_pixels) | Output units: erg/s/cm^2/arcsec^2]output_radial_cubes– Output radial spectral data cubes. [Default value: false | Dimensions: (n_cameras, n_radial_cube_pixels, n_radial_cube_bins) | Output units: erg/s/cm^2/arcsec^2/angstrom]output_radial_images2– Output statistical moment radial images, e.g. to estimate convergence statistics as the relative error is approximately \(\sqrt{\text{radial\_images2}} / \text{radial\_images}\). [Default value: false | Dimensions: (n_cameras, n_radial_pixels) | Output units: erg^2/s^2/cm^4/arcsec^4]
The following parameters produce intrinsic or attenuation only images:
output_mcrt_emission– Output intrinsic emission without transport based on MCRT sampling (also works for radial images). [Default value: false | Dimensions: (n_cameras, nx_pixels, ny_pixels) | Output units: erg/s/cm^2/arcsec^2]output_mcrt_attenuation– Output attenuated emission without scattering based on MCRT sampling (also works for radial images). [Default value: false | Dimensions: (n_cameras, nx_pixels, ny_pixels) | Output units: erg/s/cm^2/arcsec^2]output_proj_emission– Output intrinsic emission without transport with ray-based imaging. [Default value: false | Dimensions: (n_cameras, nx_pixels, ny_pixels) | Output units: erg/s/cm^2/arcsec^2]output_proj_attenuation– Output attenuated emission without scattering with ray-based imaging. [Default value: false | Dimensions: (n_cameras, nx_pixels, ny_pixels) | Output units: erg/s/cm^2/arcsec^2]
Note
The intrinsic and attenuation only images do not require scattering. Therefore, the projection outputs are preferred as they employ a ray-based quadtree imaging method for a noiseless solution with adaptive spatial convergence.
The following parameters produce spatially integrated camera frequency moments [Dimensions: n_cameras]:
output_escape_fractions– Output camera escape fractions. [Default value: true]output_freq_avgs– Output camera frequency averages. [Default value: false | Output units: freq]output_freq_stds– Output frequency standard deviations. [Default value: false | Output units: freq]output_freq_skews– Output frequency skewnesses. [Default value: false]output_freq_kurts– Output frequency kurtoses. [Default value: false]
The following parameters produce camera frequency moments for each image pixel [Dimensions: (n_cameras, nx_pixels, ny_pixels)]:
output_freq_images– Output average frequency images. [Default value: false | Output units: freq]output_freq2_images– Output frequency^2 images. [Default value: false | Output units: freq^2]output_freq3_images– Output frequency^3 images. [Default value: false | Output units: freq^3]output_freq4_images– Output frequency^4 images. [Default value: false | Output units: freq^4]
The following parameters produce camera frequency moments for each radial image pixel [Dimensions: (n_cameras, n_radial_pixels)]:
output_freq_radial_images– Output average frequency radial images. [Default value: false | Output units: freq]output_freq2_radial_images– Output frequency^2 radial images. [Default value: false | Output units: freq^2]output_freq3_radial_images– Output frequency^3 radial images. [Default value: false | Output units: freq^3]output_freq4_radial_images– Output frequency^4 radial images. [Default value: false | Output units: freq^4]
The following parameters are useful for on-the-fly false color imaging:
output_rgb_images– Output flux-weighted frequency RGB images. Note: The normalized image log intensity can be used as the alpha opacity of the image to give a nice illustration of the spectral data cube. [Default value: false | Dimensions: (n_cameras, nx_pixels, ny_pixels, 3) | Output units: RGB color]output_rgb_radial_images– Output flux-weighted frequency RGB radial images. [Default value: false | Dimensions: (n_cameras, n_radial_pixels, 3) | Output units: RGB color]output_rgb_map– Output flux-weighted frequency RGB Healpix map. [Default value: false | Dimensions: (12 * n_side_map^2, 3) | Output units: RGB color]rgb_freq_range– Frequency extrema in [-1000 1000] format. [Default value: (-1000,1000) | Units: freq]rgb_freq_min– Frequency range minimum. [Default value: -1000 | Units: freq]rgb_freq_max– Frequency range maximum. [Default value: 1000 | Units: freq]adjust_camera_frequency– Adjust frequencies for each camera based on offsets from a file. Note: This was implemented to center the RGB and other cameras for Lyα on the Hα line center. Thus, the file must have a dataset called “freq_avgs” of length n_cameras. [Default value: false]freq_offset_file– Frequency offset file (optional). [Default value:init_file]freq_offset_dir– Frequency offset directory (optional). [Default value:init_dir]freq_offset_base– Frequency offset file base (optional). [Default value:init_base]freq_offset_ext– Frequency offset file extension (optional). [Default value: hdf5]
Healpix Binning Parameters
The following parameters are related to line-of-sight Healpix binning options:
n_exp_map– Healpix exponent for the line-of-sight map, resulting in \(12 \times 4^{n_\text{exp,map}}\) directions. Note: Similar setup forn_exp_flux,n_exp_radial, andn_exp_cube. [Default value: 2 | Valid range: n_exp_map >= 0]n_side_map– Healpix number of base pixel subdivisions for the line-of-sight map, resulting in \(12 \times n_\text{side,map}^2\) directions. Note: Similar setup forn_side_flux,n_side_radial, andn_side_cube. [Overrides n_exp_map | Default value: 4 | Valid range: n_side_map >= 1]n_map_bins– Number of frequency bins for the line-of-sight flux map. Note: Similar setup forn_cube_map_bins. [Default value: 100]map_freq_range– Frequency extrema in [-1000 1000] format for the line-of-sight flux map. Note: Similar setup forcube_map_freq_range. [Default value: (-1000,1000) | Units: freq]map_freq_min– Frequency range minimum for the line-of-sight flux map. Note: Similar setup forcube_map_freq_min. [Default value: -1000 | Units: freq]map_freq_max– Frequency range maximum for the line-of-sight flux map. Note: Similar setup forcube_map_freq_max. [Default value: 1000 | Units: freq]map_radius– Radius for the line-of-sight Healpix map of radial surface brightness images. Note: Similar setup forcube_map_radius. [Units: cm]map_radius_bbox– Radius for the line-of-sight Healpix map of radial surface brightness images. Note: Similar setup forcube_map_radius_bbox. [Units: bounding box]n_map_pixels– Number of radial pixels for the line-of-sight Healpix map of radial surface brightness images. Note: Similar setup forn_cube_map_pixels. [Default value: 100]map_pixel_width– Intrinsic width of each radial pixel for the line-of-sight Healpix map of radial surface brightness images. Note: Similar setup forcube_map_pixel_width. [Units: cm]map_pixel_arcsec– Observed angular width of each radial pixel for the line-of-sight Healpix map of radial surface brightness images. Note: Similar setup forcube_map_pixel_arcsec. [Units: arcseconds]output_map– Output a line-of-sight Healpix map of escape fractions. [Default value: false | Dimensions: (12 * n_side_map^2)]output_map2– Output statistical moment line-of-sight Healpix map, e.g. to estimate convergence statistics as the relative error is approximately \(\sqrt{\text{map2}} / \text{map}\). [Default value: false | Dimensions: (12 * n_side_map^2)]output_flux_map– Output a line-of-sight Healpix map of spectral fluxes. [Default value: false | Dimensions: (12 * n_side_flux^2, n_map_bins) | Output units: erg/s/cm^2/angstrom]output_radial_map– Output a line-of-sight Healpix map of radial surface brightness images. [Default value: false | Dimensions: (12 * n_side_radial^2, n_map_pixels) | Output units: erg/s/cm^2/arcsec^2]output_cube_map– Output a line-of-sight Healpix map of radial spectral data cubes. [Default value: false | Dimensions: (12 * n_side_cube^2, n_cube_map_pixels, n_cube_map_bins) | Output units: erg/s/cm^2/arcsec^2/angstrom]
The following parameters produce frequency moments for each Healpix map pixel [Dimensions: 12 * n_side_map^2]:
output_freq_map– Output average frequency map. [Default value: false | Output units: freq]output_freq2_map– Output frequency^2 map. [Default value: false | Output units: freq^2]output_freq3_map– Output frequency^3 map. [Default value: false | Output units: freq^3]output_freq4_map– Output frequency^4 map. [Default value: false | Output units: freq^4]
Advanced Parameters
The following parameters are related to advanced options:
two_level_atom– Line radiative transfer incorporates occupation number densities from both lower and upper transitions. If this is false then we assume that bound electrons are always in the ground state. Note: This currently also switches from a Voigt to a Gaussian line profile, and assumes complete redistribution for scattering. [Default value: false]resonant_scattering– Turn resonant scattering on/off. Note: It is not recommended to override this option unless you know exactly what you are doing. [Default value: Based on line]load_balancing– Use MPI load balancing algorithms. Note: Due to the OpenMP load balancing this is not recommended in general as the number of MPI tasks is usually much smaller than the number of photon packets. [Default value: false]