Dense matrix time out for 3D

For confined 3D structures the dense matrix isn't properly created when the number of boundary nodes is above several hundreds of nodes. Looks that it is time outed and python never gets reply from the C routines. I will chop the nester for loops in blocks, as I originally did in the preprocessing of TetraMag.

To upload designs, you'll need to enable LFS and have an admin enable hashed storage. More information