Danny,
I've never run Cart3D 'manually'. When I want to run a case with no
adaptation, I still use aero.csh, but I just turn off adaptation. If
your Cart3D distribution is different, this won't work for you.
You'll probably have better luck asking on the Cart3D group, but I'll
give it a shot.
In your commands.csh, you do this...
set y_is_spanwise = -y_is_spanwise
But, flowcart does not read variables like this from the environment.
I believe everything is passed to flowcart on the command line. I
believe the actual execution of flowCart happens on line 659 of
aero.csh as downloaded from the Wiki.
( $timer $flowCart $verb -his -N $it_fc -T $binaryIO -clic
$mg_gs_fc $mg_levs -limiter $limiter -tm $tm -cfl $cfl $y_is_spanwise
$fc_restart $fmg $blcc $buffLim $subcell >> cart3d.out ) >&! $timeInfo
It is a mess, but you can see that the variable $y_is_spanwise is
passed to flowcart on the command line.
So, I would try this in your script....
flowCart -mg 4 -N 100 -his -T -clic -v -y_is_spanwise
Rob