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My first guess is that you have negative throat lengths due to pores being too large for the lattice (i.e. overlapping). You can see if this is the case by doing:
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I created a simple pore network, where the pores on the left and right of the network were larger than the remaining pores by a magnitude of 10. I set the inlet and outlet as the left and right boundaries.
I was just trying to understand why the saturation of the invading phase decreases at some points, any insight would be appreciated.
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