Input parameters for Alfjup3d.f90:

nrun: run number.  In the zip file, the results from a run are in a folder called run??? where ??? is the 3-digit run number
colatmin: Co-latitude of poleward most field line
colatmax: Co-latitude of equatorward field line
nx: number of cells in x (poloidal) direction 
ny: number of cells in y (azimuthal) direction
mltmin: Minimum Magnetic Local Time (24 hour basis) of simulated volume
mltmax: Maximum MLT
dsmin: Minimum grid spacing in parallel direction (near the ionosphere) in terms of path length measured in Jovian radii
dsmax: Maximum grid spacing 
rmax: Maximum rho value to simulate, based on equatorward field line
cour: Courant number, must by < 1 for stability
courepar: Courant number for parallel calculations
tmax: maximum time of simulation
dtplot: time interval between data dumps
ixdrive: parameter to determine shape of imposed potential is x direction:
1: uniform (no field)
2: tanh (single pulse in electric field)
3: sech (balanced pulse in electric field)
4: sinusoidal variation
5: ln cosh (tanh like pulse in electric field)
iydrive: shape of imposed potential in y direction (same as ixdrive, but option 5 not implemented)
itdrive: time evolution of input:
1: sine wave
2: pulse
3. ramp (tanh)
4: spectrum of waves
5: wave packet
6: damped sine wave
izdrive: location of driver: 0 = ionosphere; 1 = at top boundary
tdrive: duration of input pulse, interpretation depends on itdrive:
itdrive=1, tdrive is period of wave
itdrive=2, tdrive is time to peak of pulse (pulse duration is 2*tdrive)
itdrive=3: tdrive is time scale of tanh
itdrive=4: tdrive is ramp-up time
itdrive=5: tdrive is time to peak of wave packet
itdrive=6: tdrive is damping time scale 
fmax: maximum frequency of waves (not used for itdrive = 1,2,3)
itdrive=4: maximum frequency of spectrum
itdrive= 5 or 6: frequency of wave
dmax: used only for itdrive=4, gives frequency interval of input waves
mlt0: center location of driver
dmlt: width of driver
edrive0: amplitude of driver, in mV/m
ihemis: 1 for northern hemisphere, -1 for south
d: current sheet width (in Rj)
a1: inner edge of current sheet (in Rj)
a2: outer edge of current sheet (in Rj)
bsheet: magnitude of current sheet (mu0*I0 in Connerney notation)
hscale: scale length for transition between dsmin and dsmax
sigp: Pedersen conductance
nion0: density at base of ionosphere
hion0: scale height of ionospheric density 
nback: minimum density in lobes
paramplot: if =1, write fullgrid.out file with grid and Alfvén speed
eparfac: scaling factor for Eparallel factor, if =1 full factors, if =0, no Eparallel is calculated
gridcalc: if =1, calculate grid, if =0, read grid files
thist: time interval for history files
nxhist,nyhist,nzhist: number of points in x,y,z direction for hist files
xhist: locations in co-lat of history files (should have nxhist elements)
yhist: locations in MLT of history files (should have nyhist elements)
zhist: locations in radial distance for history files (should have nzhist elements)
(The history files have names like hist123.out, which would be the history plots for  xhist(1),yhist(2),zhist(3))