Does it include the correct equilibrium with atmospheric CO2, ie 420 ppm?
I'm no expert on the program. But I have consulted it with an expert who uses it to teach hydrogeologists. After his revision, I use the following input data:

The "Equilibrium_phases" line is set to equilibrium with atmospheric CO2. I don't know if this is correct (the professor advised me to do it this way).
When you run the program with this input, it will show you two states: one before the equilibrium and one after => see
the output. The average aquarist will probably get a headache out of this though, because all the concentrations are in
moles, whereas we are used to
ppm.
So, for example, 1,622e-04 M HCO3 = 0.0001622 M = 0.1622 mM = 9.9 ppm HCO3 (0.1622 M * 61.0168 g/mol HCO3).
Among other things, you can find out what kinds of compounds you get when you add various chemicals (in my case I think it was NH4NO3, H3PO4, K2CO3, CaCO3, K2SO4, MgSO4, MgCl2, CaSO4, CaCl2 and some micros) and which ones stay dissolved vs. which ones precipitate out (and in what amounts). This can be read from the "Saturation indices" section at the end of the output file. All compounds with a
negative value will remain dissolved in the water, whereas all compounds with a
positive value will precipitate out.
[So you can see, for example, that some iron in the form of Fe(OH)3, FeOOH and Fe2O3 precipitated out of my water, and manganese was similarly affected.] It's probably good to take this with a grain of salt though, because (as I mentioned) all of these outputs are only valid in pure/dead water).
PS: Sorry, Joe, for the off-topic post.