bug fixes: kchunk3d ignored, hailwat uninitialized in dycore, tile_nu…

…m wrong for nests (NOAA-EMC#806)

* nesting fixes
1. Initialize hailwat index in dynamical core.
2. Use the correct tile number for nests in atmos_model.F90.

* remove unneeded write statements

* Fix kchunk3d in io/module_write_netcdf.F90

---------

Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>

atmos_model.F90

@@ -582,7 +582,8 @@ subroutine atmos_model_init (Atmos, Time_init, Time, Time_step)
    call atmosphere_diag_axes (Atmos%axes)
    call atmosphere_etalvls (Atmos%ak, Atmos%bk, flip=flip_vc)
 
-   call atmosphere_control_data (isc, iec, jsc, jec, nlev, p_hydro, hydro, tile_num)
+   tile_num=-1
+   call atmosphere_control_data (isc, iec, jsc, jec, nlev, p_hydro, hydro, global_tile_num=tile_num)
 
    allocate (Atmos%lon(nlon,nlat), Atmos%lat(nlon,nlat))
    call atmosphere_grid_ctr (Atmos%lon, Atmos%lat)

io/module_write_netcdf.F90

@@ -407,7 +407,7 @@ end function nf_set_log_level
                if (is_cubed_sphere) then
                   chunksizes = [im, jm, lm, tileCount, 1]
                else
-                  chunksizes = [ichunk3d(grid_id), jchunk3d(grid_id), fldlev(i), 1]
+                  chunksizes = [ichunk3d(grid_id), jchunk3d(grid_id), min(kchunk3d(grid_id),fldlev(i)), 1]
                end if
                ncerr = nf90_def_var_chunking(ncid, varids(i), NF90_CHUNKED, chunksizes) ; NC_ERR_STOP(ncerr)
             end if