Does DFNFlowEngine only be used to simulate cube or cylinder models

Hi everyone:
I have a question with DFNFLOWEngine. I want to use DFNFlowEngine to simulate a cube model with a tunnel, but there are always problems, like
negative volume for an ordinary pore (temp warning, should still be safe)
CHOLMOD warning: matrix not positive definite. file: ../Supernodal/t_cholmod_super_numeric.c line: 911
something went wrong in Cholesky factorization, use LDLt as fallback this time1.

So my question is :Can DFNFLOWEngine simulate the irregular model? like a cube model with a tunnel.

If you have some ideas I would be more than grateful!

Best