IMPORTANT: Few corrections

[arango]

I have been working on a big ROMS update for the last three weeks but I am still not ready to release it. Some users have reported few problems, so here I am including few important updates:

• Modified logic on how to initialize the structure BRY_CONTACT in mod_nesting.F with the correct nested grid contact points information. I have been looking for a generic way to code this. I have rewritten this logic several times so it can handle all the possible nesting capabilities. I think that we need to compute the information for the conjugate contact region (CRR) points at the same time of the regular contact points. I hope that this logic is now robust and I don't have to change it again.

• Added couple of CPP options for nesting:

NO_CORRECT_TRACER: Switch to avoid correcting coarser grid tracers next (outside) to the physical of the boundary of the finer grid in two-way refinement. See routine correct_tracer in nesting.F for details. The default behavior is to correct the tracer values so this option can be used to turn off such two-way adjustment.

TIME_INTERP_FLUX: Switch to time interpolate coarser grid mass flux when computing finer grid boundary conditions for (ubar, vbar) in the finner grid physical boundary in routine put_refine2d. The default is to persist in time the coarser grid mass flux during the RefineScale sub-timesteps.

• A safeguard is added to routine z_weights in nesting.F to bound i-1, i+1, j-1, and j+1 operations. Their values are bounded to the maximum possible values at the edge of the contact region. In such cases, Hweight(1,m)=1 and Hweight(2:3,m)=0. This is done to avoid out of range errors. This is relevant in mosaic grids when the vertical interpolation is activated. That is, interpolate = 1 in the input contact points NetCDF file. For example, for the RHO-points we have:

              DO Kdg=1,N(dg)
                DO m=1,Npoints
                  Idg  =Rcontact(cr)%Idg(m)
                  Idgp1=MIN(Idg+1, BOUNDS(dg)%UBi(-1))
                  Jdg  =Rcontact(cr)%Jdg(m)
                  Jdgp1=MIN(Jdg+1, BOUNDS(dg)%UBj(-1))
                  IF (((IminD.le.Idg).and.(Idg.le.ImaxD)).and.            &
       &              ((JminD.le.Jdg).and.(Jdg.le.JmaxD))) THEN
                    Zd(1,Kdg,m)=GRID(dg)%z_r(Idg  ,Jdg  ,Kdg)
                    Zd(2,Kdg,m)=GRID(dg)%z_r(Idgp1,Jdg  ,Kdg)
                    Zd(3,Kdg,m)=GRID(dg)%z_r(Idgp1,Jdgp1,Kdg)
                    Zd(4,Kdg,m)=GRID(dg)%z_r(Idg  ,Jdgp1,Kdg)
                  END IF
                END DO
              END DO
  

• Corrected minor bug in extract_sta.F. Many thanks to Kelly Kearney ​bringing this to my attention.

• Corrected an adjoint bug in ad_npzd_iron.h. The variables ad_ExpAtt and ad_Itop need to be initialized to zero at the top of the routine. Many thanks to Paul Mattern for ​reporting this problem.

• Updated the contact NetCDF files (dogbone_ngc_composite.nc and dogbone_ngc_refined.nc) for the DOGBONE test case.

• Updated few files in the test reposiotry.