Hello Akash:
I've looked at your file and Marton's modification. I realized that the way Marton has defined the two middle facets with holes is such that the one on the bottom faces up, instead of down. You can reverse its normal by selecting it and pressing Ctrl-N (or using the equivalent command "Swap normal" in the "Facet" menu.
Whenever you define a facet with a hole by using the "Create two facets..." "Difference" in the "Facet" menu you should always check that the normal vector points in the direction you want, and not the reversed one. This is because the normal depends, I think... Marton correct me if I/m wrong, from the way thetwo initial facets are defined, and which vertices are chosen as the 3 first vertices in the definition of the facet with hole.
You don't see the "conical shaped particle trajectories" because the sticking coefficient of your pumping facet is very low (a bit more than 0.03), and therefore the molecules have a large probability to travel in all directions, and even come back to the upper half of the system.
If you change the sticking to 1, equivalent to a pump of almost 1000 l/s instead of the 30 l/s you've set, then you can see the shape of the molecules passing through the circular hole.
Note that since your source of the molecules is the small rectangular facet on top of the system, and it faces the hole in the middle at a small distance from it, the angular distribution of the molecules going through the hole is not a cosine-like shape, but rather it has a peak at small angles... i.e. an "excess" of trajectories with directions close to the axis of the system (Y axis).
In order to visualize this, I have set all facets to texture at 1 mm texture size (i.e. Resolution=10), and set to angular profile the two transparent facets representing the hole's entrance and exit. I have reversed their normal vector upwards. In the screenshot you can see the angular profile calculated on them, and you can see that there is an "excess" towards small angles, a bump in the curves which should otherwise resemble a sine function (because the "surface to volume" conversion box has not been checked).
By setting the min and max value in the texture scaling pane I can visualize the varying impingement rate across the pumping facet, you can see that there is a circular area in the middle getting more hits than the peripheral area near the walls of the cylinder.
Here is the screenshot, in dropbox, faster for me to do it like this:
https://www.dropbox.com/s/n0wbg25gz2z8499/Akhash.JPG?dl=0
Cheers,
Roberto