AbsorptionSpectrum

For documentation on the main interface to spectrum creation in Trident, see Spectrum Generation.

The AbsorptionSpectrum is the internal class for creating absorption spectra in Trident from LightRay objects. The AbsorptionSpectrum and its workhorse method make_spectrum() return two arrays, one with wavelengths, the other with the normalized flux values at each of the wavelength values. It can also output a text file listing all important lines.

Method for Creating Absorption Spectra

Once a LightRay has been created traversing a dataset using the Light Ray Generator, a series of arrays store the various fields of the gas parcels (represented as cells) intersected along the ray. AbsorptionSpectrum steps through each element of the LightRay’s arrays and calculates the column density for desired ion by multiplying its number density with the path length through the cell. Using these column densities along with temperatures to calculate thermal broadening, voigt profiles are deposited on to a featureless background spectrum. By default, the peculiar velocity of the gas is included as a doppler redshift in addition to any cosmological redshift of the data dump itself.

Subgrid Deposition

For features not resolved (i.e. possessing narrower width than the spectral resolution), AbsorptionSpectrum performs subgrid deposition. The subgrid deposition algorithm creates a number of smaller virtual bins, by default the width of the virtual bins is 1/10th the width of the spectral feature. The Voigt profile is then deposited into these virtual bins where it is resolved, and then these virtual bins are numerically integrated back to the resolution of the original spectral bin size, yielding accurate equivalent widths values. AbsorptionSpectrum informs the user how many spectral features are deposited in this fashion.

Creating an Absorption Spectrum

Initialization

To instantiate an AbsorptionSpectrum object, the arguments required are the minimum and maximum wavelengths (assumed to be in Angstroms), and the number of wavelength bins to span this range (including the endpoints)

from trident.absorption_spectrum.absorption_spectrum import AbsorptionSpectrum

sp = AbsorptionSpectrum(900.0, 1800.0, 10001)

Adding Features to the Spectrum

Absorption lines and continuum features can then be added to the spectrum. To add a line, you must know some properties of the line: the rest wavelength, f-value, gamma value, and the atomic mass in amu of the atom. That line must be tied in some way to a field in the dataset you are loading, and this field must be added to the LightRay object when it is created. Below, we will add the H Lyman-alpha line, which is tied to the neutral hydrogen field (‘H_p0_number_density’).

my_label = 'HI Lya'
field = 'H_p0_number_density'
wavelength = 1215.6700 # Angstroms
f_value = 4.164E-01
gamma = 6.265e+08
mass = 1.00794

sp.add_line(my_label, field, wavelength, f_value, gamma, mass, label_threshold=1.e10)

In the the call to add_line() the field argument tells the spectrum generator which field from the ray data to use to calculate the column density. The label_threshold keyword tells the spectrum generator to add all lines above a column density of 10 ¹⁰ cm ^-2 to the text line list output at the end. If None is provided, as is the default, no lines of this type will be added to the text list.

Continuum features with optical depths that follow a power law can be added with the add_continuum() function. Like adding lines, you must specify details like the wavelength and the field in the dataset and LightRay that is tied to this feature. The wavelength refers to the location at which the continuum begins to be applied to the dataset, and as it moves to lower wavelength values, the optical depth value decreases according to the defined power law. The normalization value is the column density of the linked field which results in an optical depth of 1 at the defined wavelength. Below, we add the hydrogen Lyman continuum.

my_label = 'HI Lya'
field = 'H_p0_number_density'
wavelength = 912.323660 # Angstroms
normalization = 1.6e17
index = 3.0

sp.add_continuum(my_label, field, wavelength, normalization, index)

Making the Spectrum

Once all the lines and continuua are added, the spectrum is made with the make_spectrum() function.

wavelength, flux = sp.make_spectrum('lightray.h5',
                                    output_file='spectrum.fits',
                                    line_list_file='lines.txt')

A spectrum will be made using the specified ray data and the wavelength and flux arrays will also be returned. If you set the optional use_peculiar_velocity keyword to False, the lines will not incorporate doppler redshifts to shift the deposition of the line features.

Three output file formats are supported for writing out the spectrum: fits, hdf5, and ascii. The file format used is based on the extension provided in the output_file keyword: .fits for a fits file, .h5 for an hdf5 file, and anything else for an ascii file.

Note

To write out a fits file, you must install the astropy python library in order to access the astropy.io.fits module. You can usually do this by simply running pip install astropy at the command line.

Generating Spectra in Parallel

Spectrum generation is parallelized using a multi-level strategy where each absorption line is deposited by a different processor. If the number of available processors is greater than the number of lines, then the deposition of individual lines will be divided over multiple processors.

Absorption spectrum creation can be run in parallel simply by adding the following to the top of the script and running with mpirun.

import yt
yt.enable_parallelism()

For more information on parallelism in yt, see Parallel Computation With yt.