Photodissociation and photoionization cross sections


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## Text file data format ##
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These files contain separate listings for continuum and line
photodissociation/ionisation. This is useful where the wavelength
dependence of a calculated electronic/vibrational transition is not
known. 

See photo.tar file with the photodissociation (.pd) and
photoionization (.pi) cross sections. The basic reference is:

E.F. van Dishoeck 1988, in Rate Coefficients in Astrochemistry, eds.
T.J. Millar and D.A. Williams (Kluwer), p. 49-72.

The format is:

- line 1:       title
- line 2:       number of discrete transitions N (5 in this case)
- line 3-3+N:   - label of transition
                - wavelength (A) 
                - pi e^2/m c^2  lambda^2 f eta (cm^2 A)  (See Eq. 2)

- line 3+N+1:   number of wavelengths M at which continuous cross section is
                specified
- line 3+N+2:   lower wavelength threshold for continuous cross section
                (cross section is zero for lambda < lambda_th)
                this is often indicated with a minus sign, or, in case
                the zero is explicitly listed as the last point, as -1.
- line 3+N+2+M: - label 
                - wavelength (A)
                - cross section (cm^2) at specific wavelengths
                  you need to make a spline fit through these points to get 
                  the continuous cross section as a function of wavelength 
                  (See Eq. 1)

Photoionization is only by continuous absorption.


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## Binary hdf5 data format ##
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In these files all lines and continuum data is combined into a single
cross section with an assumed wavelength dependence for calculated
vertical transitions.

The hdf5 files are made of the following data sets:

- README                A description of the data contents of this
                        file and references to the cross sections.
- wavelength            Wavelength scale (nm)
- photoabsorption       Photoabsorption cross section (cm2)   
- photodissociation     Photodissociation cross section (cm2) 
- photoionisation       Photoionisation cross section (cm2)

To extract the data on the command line using the h5tools package (in
most linux distributions):

    h5dump -d data_set_name filename.hdf5


A an example of how to extract the binary data into a python program:

    ## necessarily libraries
    import h5py
    import numpy as np
    ## open the file
    x = h5py.File('filename.hdf5','r')
    ## print all data fields
    keys = [t for t in x.keys()]
    print(keys)
    print()
    ## load the README text
    README = x['README'].value
    print( README)
    ## load data as a numpy array
    wavelength = x['wavelength'].value
    photodissociation = x['photodissociation'].value




######################################################
## Text files with combined line and continuum data ##
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For simpler usage the same data as in the binary files are also given
in simple text files. As an example of the format take the file
H2O.txt:

   # H2O cross sections
   # From the Leiden database for photodissociation and photoionization of astrophysically relevant molecules, http://home.strw.leidenuniv.nl/~ewine/photo/
   # File last modified by Alan Heays 2017-03-01
   # references: smith1981 10.1086/159359, chan1993d 10.1016/0301-0104(93)85078-M, yoshino1996 10.1016/0301-0104(96)00210-8, yoshino1997 10.1016/S0301-0104(96)00381-3, parkinson2003 10.1016/S0301-0104(03)00361-6, fillion2003 http://stacks.iop.org/0953-4075/36/i=13/a=308, fillion2004 10.1063/1.1652566, mota2005 10.1016/j.cplett.2005.09.073, harrevelt2008 10.1021/jp711857w,
   # wavelength        -- Wavelength (nm)
   # photoabsorption   -- Photoabsorption cross section (cm2)
   # photodissociation -- Photodissociation cross section (cm2)
   # photoionisation   -- Photoionisation cross section (cm2)
   # wavelength   photoabsorption photodissociation   photoionisation
      6.2000000       3.65000e-19       0.00000e+00       3.65000e-19
      6.2600000       3.82000e-19       0.00000e+00       3.82000e-19
      6.3300000       4.17000e-19       0.00000e+00       4.17000e-19
      6.3900000       4.01000e-19       0.00000e+00       4.01000e-19
      6.4600000       4.51000e-19       0.00000e+00       4.51000e-19
      ... more data...