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Hi William,
Thanks for posting your files, it makes it a lot easier to find problems.
I think your issue stems from your window surface being coincident with a wall surface. When to surfaces with different materials overlap, the surface found first in the ray intersection check is the one that is used and the other ignored. The first surface to be found is essentially random, but generally repeatable for the same exact simulation.
Instead of using this completely enclosed box for your room with the window overlapping one surface like this:
!genbox wall_mat room 4 5 3 | xform -t 0 0 8
win_mat polygon window
0
0
12 4 0 9
4 0 11
0 0 11
0 0 9
Try using separate boxes for each wall like this:
#This first wall is only 1m tall to make room for the window above:
!genbox wall_mat room 4 0.1 1 | xform -t 0 -0.1 8
!genbox wall_mat room 4 0.1 3 | xform -t 0 5 8
!genbox wall_mat room 0.1 5.2 3 | xform -t -0.1 -0.1 8
!genbox wall_mat room 0.1 5.2 3 | xform -t 4 -0.1 8
!genbox ceiling_mat room 4.2 5 0.1 | xform -t -0.1 -0.1 11
!genbox floor_mat room 4.2 5 0.1 | xform -t -0.1 -0.1 -0.1
win_mat polygon window
0
0
12 4 0 9
4 0 11
0 0 11
0 0 9
Also, a ground plane of 20km is maybe a bit bigger than is necessary for this simulation. The downside of having a 20km scene when you only care about 5 meters of the scene is poor ambient cache performance. you could either turn off the ambient cache with -aa 0 (which I'd also encourage decreasing -lw, and increasing -ad ), or you could make the ground plane and obstructions 40m instead.
Andy