cross_sections

For each UV spectrum that you want to include in the chemical modelling, you will need to specify a cross sections data file. This contains the various photoionisation cross sections, shielding factors, and photoheating rates for each photo-chemical reaction, averaged over the given spectrum. Quantities corresponding to individual reactions are organised into the same reaction groups as used in chimes_main_data.hdf5 (see the chimes_main_data section for more details). Note that CHIMES assumes that the reactions in each group are arranged in the same order in chimes_main_data.hdf5 and the individual cross sections data files.

The chimes-data repository includes several cross sections data files for commonly used spectra, including the Black (1987) local interstellar radiation field (cross_Sections_B87.hdf5), the Sazonov et al (2004) average quasar spectrum (cross_sections_S04.hdf5), the redshift-dependent extragalactic backgrounds from Haardt & Madau (2001) (HM01_cross_sections/), Haardt & Madau (2012) (HM12_cross_sections/) and Faucher-Giguere (2020) (FG19_cross_sections/). We also include several UV spectra from a single stellar population using Starburst 99 models (Leitherer et al. 2014) at different stellar ages (starburstCrossSections/; see Richings et al. 2022 for details).

If you want to include your own UV spectra in CHIMES, you will need to create the corresponding cross sections file. This can be done using the generate_cross_sections.py python script from the chimes-tools repository (see the Generate Cross Sections section). Be aware that the photon energy bands over which the cross sections are defined will depend on whether RT coupling has been switched on (see the Coupling to a Radiative Transfer Solver section).

The data arrays included in the cross sections files are described in more detail below.

photoion_fuv

Photoionisation of species with an ionisation energy <13.6 eV.

Data Array Description
N_reactions
A 1-dimensional array of length 2 containing the number of reactions in
this group. The first number gives the number of reactions that do not
involve molecules, while the second number gives the total number of
reactions, including molecules.
sigmaPhot
A 1-dimensional array of length N_reactions that gives the
photoionisation cross section of each reaction, averaged over the given
UV spectrum (see equation 2.5 in Richings et al. 2014a).
epsilonPhot
A 1-dimensional array of length N_reactions that gives the spectrum-
averaged excess energy of ionising photons in the optically thin limit,
used to calculate the photoheating rate (see equation 3.6 in Richings et
al. 2014a).

photoion_euv

Photoionisation of species with an ionisation energy >13.6 eV.

Data Array Description
N_reactions
A 1-dimensional array of length 2 containing the number of reactions in
this group. The first number gives the number of reactions that do not
involve molecules, while the second number gives the total number of
reactions, including molecules.
sigmaPhot
A 1-dimensional array of length N_reactions that gives the
photoionisation cross section of each reaction, averaged over the given
UV spectrum (see equation 2.5 in Richings et al. 2014a).
shieldFactor_1D
A 3-dimensional array of length (N_reactions x 3 x
N_Column_densities). In the second dimension of this array, index 0
contains the factor S_gas1 from equation 3.8 of Richings et al.
(2014b) for each reaction as a function of HI column density, for
calculating the shielded photoionisation rates; while indices 1 and 2
contain the first integrals in the numerator and denominator,
respectively, of equation 3.22 in Richings et al. (2014b) for each
reaction as a function of HI column density, for calculating the shielded
photoheating rates.
shieldFactor_2D
A 4-dimensional array of length (N_reactions x 6 x
N_Column_densities x N_Column_densities). In the second dimension
of this array, indices 0 and 1 contain the factors S_gas2 and
S_gas3 from equation 3.8 of Richings et al. (2014b) for each reaction,
for calculating the shielded photoionisation rates. Indices 2-5 contain
the second and third integrals in the numerator and denominator of
equation 3.22 in Richings et al. (2014b) for each reaction, for
calculating the shielded photoheating rates.

photoion_auger_fuv

Auger photoionisation of species with an ionisation energy <13.6 eV.

Data Array Description
N_reactions
A 1-dimensional array of length 2 containing the number of reactions in
this group. The first number gives the number of reactions that do not
involve molecules, while the second number gives the total number of
reactions, including molecules.
sigmaPhot
A 1-dimensional array of length N_reactions that gives the
photoionisation cross section of each reaction, averaged over the given
UV spectrum (see equation 2.5 in Richings et al. 2014a).

photoion_auger_euv

Auger photoionisation of species with an ionisation energy >13.6 eV.

Data Array Description
N_reactions
A 1-dimensional array of length 2 containing the number of reactions in
this group. The first number gives the number of reactions that do not
involve molecules, while the second number gives the total number of
reactions, including molecules.
sigmaPhot
A 1-dimensional array of length N_reactions that gives the
photoionisation cross section of each reaction, averaged over the given
UV spectrum (see equation 2.5 in Richings et al. 2014a).

General Spectrum Data

The following data arrays contain general information about the given UV spectrum, and are found in the root of the cross sections HDF5 data file.

Data Array Description
isotropic_photon_
density
The number density of photons in units of photons cm^-3. The photon
flux, in units of photons cm^-2 s^-1, can then be found by
multiplying isotropic_photon_density by the speed of light. The
energy band over which the photon density is defined depends on whether
RT coupling is switched on. If RT coupling is disabled (the standard
mode), then the photon density is defined over all hydrogen-ionising
photons, i.e. those with energies >13.6 eV, for each UV spectrum.
However, if RT coupling is switched on, the photon density is defined
only for that particular energy bin. See the
Coupling to a Radiative Transfer Solver section for details.
We have included this parameter in the data files for convenience.
However, the user is free to set the corresponding
isotropic_photon_density parameter in the gasVariables
structure to a different value if they wish, for example to vary the
strength of the radiation field compared to the fiducial value given
in the data files.
G0_parameter
The strength of the radiation field in the 6-13.6 eV band, G0, in
Habing units, divided by the photon flux, i.e.:
G0_parameter = G0 / (isotropic_photon_density *
speed_of_light).
H2_dissocJ
The strength of the radiation field in the 12.24-13.51 eV band, defined as
the number density of photons in this band divided by the
isotropic_photon_density parameter times the speed of light. This is
used to calculate the photodissociation rate of H2.

TableBins

The TableBins group contains the Column Density table bins that are used to tabulate and interpolate the various shielding factor arrays.