updating to have some test cases to run. Currently test1 works and there is a figure to compare with in the examples directory. Still working out some other problems including the s isoslice and 3d options at the moment (something changed just recently causing trouble).
There was a bug when converting the indices back from fortran indexing to python indexing in the run loop. there was also a bug in readfields for a z depth isoslice in which the dzt calculation using isoslice had the input arguments switched in order such that the whole array ended up masked out.
I do not remember what this branch was originally for, but I did some changes in readfields to improve the speed. The interpolation, flipping of arrays, and depth calculations should all be improved for speed if possible.
switched so that choices in run (3d/2d and turbulence/diffusion type) are chosen with flags in run.py instead of through compiler flags. Also worked on a problem in the anisodiffusion scheme.