genSting: Convert Stingray Outputs to SEDs

In asgr/Viperfish: SEDs with Shark or Stingray

Convert Stingray Outputs to SEDs

Description

Takes Stingray light cones and converts to apparent and absolute SEDs.

Usage

genSting(file_sting = NULL, path_shark = ".", path_out = ",", 
    h = "get", cores_per_subvolume = 1, cores_per_snapshot = 4, 
    children_outfile = "/dev/null", filters = c("FUV_GALEX", 
        "NUV_GALEX", "u_SDSS", "g_SDSS", "r_SDSS", "i_SDSS", 
        "Z_VISTA", "Y_VISTA", "J_VISTA", "H_VISTA", "K_VISTA", 
        "W1_WISE", "W2_WISE", "W3_WISE", "W4_WISE", "P100_Herschel", 
        "P160_Herschel", "S250_Herschel", "S350_Herschel", "S500_Herschel"), 
    tau_birth = 1.5, tau_screen = 0.5, pow_birth = -0.7, pow_screen = -0.7, 
    alpha_SF_birth = 1, alpha_SF_screen = 3, alpha_SF_AGN = 0, 
    emission = FALSE, stellarpop = "BC03lr", read_extinct = FALSE, 
    sparse = 5, time = NULL, mockcone = NULL, intSFR = TRUE, 
    final_file_output = "Stingray-SED.csv", temp_file_output = "temp.csv", 
    extinction_file = "extinction.hdf5", addradio_SF = FALSE, 
    waveout = seq(2, 30, by = 0.01), ff_frac_SF = 0.1, ff_power_SF = -0.1, 
    sy_power_SF = -0.8, reorder = TRUE, restart = FALSE, verbose = TRUE, 
    write_final_file = FALSE, mode = "photom", spec_range = c(3600,9600)) 

getSFHfull(file_sting = "mocksurvey.hdf5", path_shark = ".", snapmax = 199,
  cores_per_subvolume = 4, verbose = TRUE)

getSFHsing(id_galaxy_sam, snapshot = NULL, subvolume = NULL, path_shark = ".")

mockcone_extract(file_sting = "mocksurvey.hdf5", reorder = TRUE)

mocksubsets(mockcone)

Arguments

file_sting	Character scalar; full path to Stingray HDF5 file. The package will check that the file exists and we have read access.
mockcone	data.table; the output of mockcone.
path_shark	Character scalar; path to top directory containing Shark outputs. The package will check that the files and path exists and we have read access.
id_galaxy_sam	Integer vector; a list of Shark SAM galaxies to be extracted from a given snapshot and subsnapshot.
h	Numeric scalar; little-h assumed in Shark (needed to convert SFRs to actual SFR since they use Msun/yr/h). If set to "get" (default) it will inherit the redshift from the target Stingray HDF5 file, which is probably what you want most of the time.
cores_per_subvolume	Integer scalar; number of cores to process a subvolume's snapshot on. This multiplied by cores_per_snapshot yields the total number of processes that will work in parallel.
cores_per_snapshot	Integer scalar; number of cores to process a snapshot's galaxies on. This multiplied by cores_per_subvolume yields the total number of processes that will work in parallel.
children_output	Character scalar; file where parallel worker's outputs will be dumped to. It is given as-is to SNOW's makeCluster.
snapmax	Integer scalar; maximum snapshot output by Shark.
filters	Character vector; filters to use for the photometry.
tau_birth	Numeric scalar; dust tau for birth clouds. Associated with sub 10 Myr star formation. See SFH.
tau_screen	Numeric scalar; dust tau for screen. See SFH.
time	Numeric vector; if provided this should be the full vector of lookback time corresponding to the time outputs in SFHlist. It should have the same length as the matrices in SFHlist have columns.
sparse	Numeric scalar; amount of sparse sampling of the spectra to make. Higher values mean coarser spectra is processed, which means less accurate photometry, but faster processing. Generally done when computing higher resolution libraries for AB mags.
intSFR	Boolean scalar; should the massfunc be intergrated between ages? This might be necessary if the SFH is quite bursty, but it is more expensive to compute and not required if the SFH is quite smooth.
final_file_output	Character scalar; name for the final output file to write to. This should not be an existing file and end ".csv" or ".hdf5".
temp_file_output	Character scalar; name for the temporary file to write to. This should not be an existing file and end ".csv".
extinction_file	Character scalar; name of file containing the extinction information. This should not be an existing file and end ".hdf5".
addradio_SF	Logical; should radio flux from star formation be included in the output?
waveout	Numeric vector; desired output log10 wavelength grid to use in Ang. See ProSpectSED.
ff_frac_SF	Numeric scalar; free-free HII nebular plasma thermal radio emission contribution fraction at 1.4 GHz used in radiocont (should be between 0.05 and 0.2 typically). By definition the fraction of radio synchrotron emission associated with star-formation at 1.4 GHz will be 1 - ff_frac_SF.
ff_power_SF	Numeric scalar; power-law slope of the free-free nebular plasma thermal radio emission associated with star-formation used in radiocont. Leave as the default (-0.1), unless you know what you are doing.
sy_power_SF	Numeric scalar; power-law slope of the synchrotron radio emission associated with star-formation used in radiocont (should be between -0.8 and -0.6 typically).
write_final_file	Logical; whether to write the output of this function into a csv file (with name specified by final_file_output) within the same directory as file_sting.
mode	Character scalar; should the output be photometry in filters (photom) or the full resolution spectrum (spectrum).
spec_range	Numeric vector; the spectral wavelength range to limit the mode = 'spectrum' output to in Angstrom.
reorder	Logical; Should the output mock cone be re-ordered so to enforce that it is first ascending in subsnapID, followed by id_galaxy_sam within groups of subsnapID? It might improve speed for this to be TRUE (meaning subsets are contiguous), but it means the ordering will be different compared to the target mockcone.
restart	Logical; should genSting read in the current temporary file (as specified by temp_file_output) and carry on from where the code terminated? This is useful if the process is killed accidentally, or hits a machine wall time for running.
verbose	Logical; should helpful verbose outputs be printed regarding the processing?
snapshot	Integer scalar; snapshot number to use.
subvolume	Integer scalar; sub-volume snapshot number to use.

Details

This interface is pretty high level, so should work fine if the paths are correct.

Note the output absolute magnitudes are rest frame, whilst the apparent magnitudes are observed frame.

The apparent and absolute magnitudes are physical assuming a fixed H0=67.8 km/s/Mpc (Planck 2018) cosmology. This cannot be changed by the user (to remove silly H0 mistakes), so you should add 5.log10(0.678) (which is -0.844) to the absolute magnitudes if you want H0=100 km/s/Mpc type magnitudes. You should not adjust the apparent magnitudes since the Universe does not look different just because we change our mind about H0, and nor should our apparent magnitudes!

Value

genSting returns a list called outSED containing a data.frame of named absolute and apparent magnitudes for bulge, disk and total photometry.

getSFHfull returns a full list of the SFRs and the Z for the bulge (disk instability and merger driven) and disk for a given Stingray mock cone. This functions use is fairly deprecated now since we instead process on the fly in genSting (maintains processing speed for large datasets), but it might be useful for other purposes so it is being left available.

getSFHsing returns a list of the SFRs and the Z for the bulge (disk instability and merger driven) and disk for a subset of galaxies for a given snapshot and subsnapshot. Also returns the id_galaxy_sam actually present, and the location of the present galaxies relative to the input id_galaxy_sam (keep).

mockcone_extract outputs the contents of a target Stingray HDF5 into an R data.table. Mostly present for use inside genSting, but currently deprecated.

mocksubsets outputs the minimally required sub-volumes and SAM galaxy ID list from a target mockcone. Mostly present for use inside an older version of genSting, but currently deprecated.

Author(s)

Aaron Robotham

See Also

genSED, genShark

Examples

## Not run: 
test_def = genSting('localtest/mocksky_19.hdf5', 'localtest/')
  
test_spec = genSting('localtest/mocksky_19.hdf5', 'localtest/', emission = TRUE,
  mode = 'spec', stellarpop = 'BC03hr')

## End(Not run)

asgr/Viperfish documentation built on July 8, 2023, 12:30 a.m.