How do we solve the geometric coincidence problem? I need a semi-cylinder that fits into the cuboid but if I use the cuboid and the cylinder directly it's geometrically problematic
I'm not quite following the question. MCNP does Constructive Solid Geometry. Shapes are supposed to intersect and then you tell it which volumes are what part of the problem.
In a cell definition a positive surface typically means above or outside. A negative surface means below or inside. If you take a look at cell 3, you have -3 4, meaning below x=4 and at the same time above x=6. The space between x=4 and 6 is "3 -4". Now have a look at cell 4 and see if you can find something similar.
However, after I corrected the error of x axis, the modeling problem still occurred in cell card 1. Why is cell card 2 and cell card 1 written in the same way? cell1 caused the problem, but cell2 did not
MCNP seems happy. When I try the interactive plotter I see the full D. VisEd does not seem happy from your picture. Maybe VisEd does not like the comment. I do not see an error.