Regions NOT forming single region in region union command – LAMMPS General Discussion

i am trying to simulate a lennard-jones gas in two cubical chambers with a cylindrical tunnel in between them to allow particles to go from on compartment to other. i have used the region union command to join the two blocks and cylinder(open 1 open 2, i mean its open on both circular faces). the problem is that particles are not going through the tunnel rather reflecting from the join as if the regions are still separate and just placed together. i don’t understand why the blocks and cylinder are not forming a single region. please help, it’s my undergrad FYP.

From your description I infer that you are trying to use fix wall/region to contain your gas atoms.
That is notoriously tricky, if not impossible, for complex compound regions as you can have plenty of ambiguities about when an atom is inside or outside which sub-region and what that means for the union of the regions.

For such complex regions it is often much easier to build a containment from explicit atoms, e.g. by having a larger region describing the outer dimensions and then deleting atoms only for a subset.

Something like this:

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