Implemented the J_ij matrix.

According to my calculations, the J_ij matrix has been added. It is
O(dimension^2) and thus, there is feedback of printed percentages added
here.
Merge remote-tracking branch 'upstream/master' into matt
Started coding W matrix and changed init behavior of the LinAl class.

- started structure of WMatrix class and started coding some of the
  terms.
- changed init behavior, so we have one init() function.
merged functions.py