So, after debugging and debugging for days, Jason and I have finally found the (hopefully) real root of our problems... we were setting up the linear system that needs to be solved to make the fluid cells divergence free completely wrong. We didn't adjust the setup from the setup of the smoke system and we've realized after some help from this paper that we need to completely alter our function setUpAMatrix(). We've figured the dimensions of our square matrix should actually be the number of cells that contain liquid, and there doesn't actually need to be a row and column for every cell in the MAC Grid as with the smoke simulation. So, we're going to have to change the implementation for our sparse matrix and pcg solver.
On a side note, while working on our Alpha Review we've realized our previous 3 step approach was completely out of order (we thought steps that came later came earlier and vice versa) so we are re-organizing our whole game plan. It's going to be a long night/couple of weeks but at least now we've figured out the main issue.
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