Allow KH_res_ind_2D initial conditions to be set

[evazlimen]

KH_res_ind() was always setting the 3D initial conditions. I added an if/else statement so that 3D initial conditions are only set if there is more than one z grid cell.

• KH_res_ind() sets 2D ICs for nz =1 and 3D ICs for nz >1
• Reduced standard runtime in the KH_res_ind_3D parameter file to t=3. Evolution is very non-linear by the old runtime of t=5 and it is not really resolution independent at that time. Up to t=3 it stays in the linear regime.
• Reduced the initial velocities for 2D and 3D KH_res_ind ICs to the velocities in KH_discontinuous_2D on advice of @brantr. Keeps this example problem simpler and makes it more resolution independent.
  I could not get clang to work on my computer sorry!

[evazlimen]

I was able to fix the clang-format issues :)