Small bug fixes in the defect code

The code produced different results depending on the position of the defect. This was because the model potential used always assumed that the defect is located at the origin. This has now been fixed such that the user can specify the position of the defect and the code the prodeuces the same result as when the defect is at the origin.

In addition, complex values were cast to real variables in various places. In reality, the numbers are always real and I have fixed it such that only the real part is passed on.

There are two issues related to this code that may be resolved after the merge

Closes #717 (closed), #556 (closed)