Misceleaneous corrections

[arango]

Several miscellaneous corrections are applied:

• Using potential/neutral (pden) density in the tracer diffusion isopycnic tensor in routines t3dmix2_iso.h and t3dmix4_iso.h. It was using in situ density (rho). Oops, I missed this one. I just discovered by looking at those routines. I thought that we were using pden.

• Correct the extraction of free-surface in shallow-water nesting applications. We need instead in nesting.F routine get_refine:

  # ifdef SOLVE3D
             CALL get_contact2d (dg, model, tile,                          &
        &                        r2dvar, 'Zt_avg1',                        &
        &                        cr, Rcontact(cr)%Npoints, Rcontact,       &
        &                        LBi, UBi, LBj, UBj,                       &
        &                        COUPLING(dg) % Zt_avg1,                   &
        &                        REFINED(cr) % zeta(:,:,tnew))
  # else
            CALL get_contact2d (dg, model, tile,                          &
       &                        r2dvar, 'zeta',                           &
       &                        cr, Rcontact(cr)%Npoints, Rcontact,       &
       &                        LBi, UBi, LBj, UBj,                       &
       &                        OCEAN(dg) % zeta(:,:,Tindex2d),           &
       &                        REFINED(cr) % zeta(:,:,tnew))
  # endif
  

• Added wet/dry mask during penetration of solar radiation into the water column in pre_step3d.F:

  #  ifdef SOLAR_SOURCE
  !
  !  Add in incoming solar radiation at interior W-points using decay
  !  decay penetration function based on Jerlov water type.
  !
            IF (itrc.eq.itemp) THEN
              DO k=1,N(ng)-1
                DO i=Istr,Iend
                  FC(i,k)=FC(i,k)+                                        &
       &                  dt(ng)*srflx(i,j)*                              &
  #   ifdef WET_DRY
       &                  rmask_wet(i,j)*                                 &
  #   endif
       &                  swdk(i,j,k)
                END DO
              END DO
            END IF
  #  endif