Cylindrical pore using region command

Dear all,

I am trying to use the region command to carve a cylindrical void out of a rectangular block located in the middle of my simulation box, as shown in the attached image. The dimensions of the block along the y and z directions are identical to that of the simulation box. Along the x direction, the simulation box bounds are -45 and 55 while those of the block are 0 and 10. The cylinder axis is along the x direction and located at y=z=0.0. The length of the cylindrical void is 10.0. I attempted to set up this geometry using the following sequence of commands:

region r2 cylinder x 0.0 0.0 v_r0 0.0 $(v_pl) units box side out

region r3 block 0.0 $(v_pl) EDGE EDGE EDGE EDGE units box

region r4 intersect 2 r2 r3 side out

Subsequently, I used the fix wall/region command as follows:

fix f1 all wall/region r4 lj126 1.0 1.0 1.0

I first computed the force exerted by the wall on a single test atom placed at the locations (-0.01,0,0) and (0.01,0,0). At the former location, the force is zero. However, I obtained a force of magnitude 10^27 acting along the positive x-direction for the latter case. This seems to suggest that the atom experiences a wall force due to the flat surface of the cylinder, which is not what I want. May I know how the above sequence of commands should be modified to get rid of this force so that particles can move freely in and out of the cylindrical void?


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are you certain, that it has to be “side out” for region r4 and not “side in”?