Fig. 7 in the libRadtran-2.0 paper was produced as follows:

NB: Make sure to set paths in the uvspec input and the Plot.py files
to match your libradtran installation.

Upper plot
----------
run uvspec with and without the line

output_quantity transmittance

in the input file spectrum_flex.inp. Store the two output files in 

UVSPEC_FLUORESCENCE_670_700_fluor.OUT
UVSPEC_FLUORESCENCE_670_700_fluor_trans.OUT

Run Plot.py with 
plot_type = 'UpperPlotFig7'


Lower plot
----------

run uvspec without the fluorescence source, that is, comment out the line

fluorescence_file ../../../libRadtran-2.0/examples/UVSPEC_FLUORESCENCE.FLU

in the input file spectrum_flex.inp.

Pipe output to the file 

UVSPEC_FLUORESCENCE_670_700_nofluor.OUT

Convolve this and the corresponding file from the upper plot with
the spectral response function:

conv UVSPEC_FLUORESCENCE_670_700_fluor.OUT SLIT_0.3.dat > UVSPEC_FLUORESCENCE_670_700_fluor.OUTc_0.3
conv UVSPEC_FLUORESCENCE_670_700_nofluor.OUT SLIT_0.3.dat > UVSPEC_FLUORESCENCE_670_700_nofluor.OUTc_0.3

Run Plot.py with 
plot_type = 'LowerPlotFig7'
