IDL routines in alfjupiar.pro (notation: bold are routine names, italics give arguments:

colorset: a routine to set up the color table

cbar, vmn, vmx, x1=x1,y2=y2,black0=black0,vcut=vcut
Routine to make a color bar:
vmn,vmx: minimum and maximum values
x1,y2: optional parameters to set position of colorbar
black0: set flag to make 0 level black
vcut: used with black0 to set limit on 0 level

st,v: a routine to quote formatted string name of variable v

unitpar,v: a routine to quote the units of variable v

readgrid,nrun: reads the grid file for run nrun

plotgrid,nrun,nfl,ngam,gread=gread
Makes a plot of the grid.  

vaplot,nrun,nogcalc=nogcalc,clip=clip
Makes a contour map of the Alfvén speed for run nrun
nogcalc is set if the grid is already been read in
clip sets clipping array.  Effect depends on number of arguments:
  1 argument: sets limits of 0,clip in both directions
  2 arguments: set limits of 0,clip[0] in radial direction and 0,clip[1] in z
  4 arguments: set limits of clip[0],clip[1] in r and clip[2],clip[3] in z

readscalefacs,nrun: reads the scalefacs file for scaling variables to ionosphere

poyntslice,nrun,mlt0,istart,iend,gread=gread,vmax=vmax,rmax=rmax
Routine to make contour map of Poynting flux for run nrun
mlt0 is value of MLT to use
istart,iend give first and last time dump to use
gread is set to read grid file
vmax if set gives maximum value of Poynting flux.  If not set, max value is used
rmax if set gives maximum radial value to plot.  If not set, max r is used

poyntsliceeps,nrun,mlt0,istart,iend,gread=gread,vmax=vmax,rmax=rmax
Like poyntslice, but writes an encapsulated postscript file instead of plotting.  Useful for movies.

phiparmax,nrun,mlt0,i0,i1,gread=gread,ymax=ymax
Routine to make plot of maximum parallel potential for run nrun
mlt0 is value of MLT to use
i0,i1 give first and last time dump to use
gread is set to read grid file
ymax if set, gives maximum value of potential.  If not set maximum of potential is used

histplot,nrun,ii,jj,kk,vars,tstart=tstart,tend=tend
Makes plot from history files.  Input to Fortran code gives history files the form hist[ii][jj][kk].out, (e.g., hist111.out) where each digit can correspond to a different nu,phi,mu combination
vars gives which variables to plot, with vars = 1 being Enu, 2=Ephi, 3=Emu, 4=Bnu, 5=Bphi, 6=Jmu
tstart, tend give starting and ending times (in seconds), default is whole run

histfft,nrun,ii,jj,kk,vars,tstart=tstart,tend=tend,fmax=fmax,nolog=nolog
Does Fourier transform of history file
Arguments the same as histplot, plus:
fmax gives maximum frequency to plot
nolog, if set, plots value of FFT; if not set, plots log of FFT

excon,alpha,eps,xmax,dx,zmax,dz
Routine for calculating E/Einc for ideal IAR model
alpha, eps are parameters of IAR model (see eqn. 2 in paper)
xmax,dx are maximum and increment of x = 2h omega/VAI parameter
zmax,dz are maximum and increment of z/h

vadenline,nrun,icolat0,rmax=rmax
Routine to make plot of Alfvén speed and density for run nrun
icolat0 gives invariant co-latitude of field line
rmax if set gives maximum r value to plot, if not set, whole simulation



Figure 1:
vadenline,37,17,rmax=3

Figure 2:
excon,18.5,.05,10,.1,25,.5

Figure 3: 
plotgrid,58,8,14

Figure 4:
vaplot,58 (for setting main plot)
Inset to figure 4 uses
vaplot,58, clip=[0,1.5,0.8,2.0]

Figure 5:
vadenline,58,17

Figure 6:
panel a: histplot,37,1,1,3,1,tend=10
panel b: histplot,37,1,1,3,5,tend=10

Figure 7:
histfft,37,1,1,3,1,fmax=5,/nolog

Figure 8:
panel a: histplot,44,1,1,3,5,tend=20
panel b: histplot,54,1,1,3,5,tend=20

Figure 9:
histplot,58,1,1,3,5

Figure 10:
phiparmax,58,0,1,600

Figure 11: (note for this run, a dump is done every 0.2 seconds, e.g. 50 means t=10
panel a: poyntslice,58,0,50,50,vmax=200
panel b: poyntslice,58,0,200,200,vmax=200
panel c: poyntslice,58,400,400,vmax=200
panel d: poyntslice,58,600,600,vmax=200

Figure 12:
phiparmax,57,0,1,600

Movie S1:
poyntsliceeps,58,0,1,600,vmax=200