Hello Wunghoa,
Unfortunately, we currently cannot plot the spectrum of secondaries in WebRun. In order to find the spectrum of secondary particles, you will have to make two GALPROP runs:
(1) one with secondary particles and
(2) one without them,
and then find the spectrum of secondaries as the total flux of (1) minus the total flux of (2).
Be careful: FITS files contain columns for "primary" and "secondary" particles, but these are not the "secondaries" in the usual sense. Those are CR particles that have undergone at least one inelastic collision. The correct way to find the flux of secondary leptons is to make two GALPROP calculations (with and without secondary leptons) and then subtract the total fluxes.
To plot the spectra, you can modify our tool PlotGalprop to suit your needs. It can be downloaded from this page
http://galprop.stanford.edu/resources.php?option=routinesand the direct link is
http://galprop.stanford.edu/download/routines/plot_galprop.py.gzThis tool is used by WebRun to make plots. Inside you can find the Solar modulation algorithm in the simple modulation potential model.