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Couple of bugs were reported in the matlab/grid/contact.m used to compute all the contact regions and contact points data for nesting.

This ticked was re-opened again because there were still couple of errors when setting mask_v. We need to have:

     C.mask_v   = G(rg).mask_v(IN);

instead of

     C.mask_v   = G(rg).mask_u(IN);

Many thanks to Chris Edwards for ​reporting this problem.

The fine2coarse2d and fine2coarse3d routine in nesting.F were rewritten in a compact way and an option for area averaging was added. We still have problems in in two-way nesting and the model becomes barotropically unstable. This is released to facilitate beta-testing. We would let you know when everything is working correctly. Please be patient... Many thanks to Chris Edwards for his help in the refinement algorithms.

Corrected a bug in mod_nesting.F when computing the open boundary switch LBC_apply in refinement applications.

• Renamed script x_etopo5.m to x_etopo.m in the matlab/bathymetry directory of the repository. This script can be used to extract any resolution ETOPO bathymetry with the following structure:

  netcdf etopo5 {
  dimensions:
          lon = 4320 ;
          lat = 2161 ;
  variables:
          float topo_lon(lon) ;
                  topo_lon:long_name = "ETOPO5 longitude" ;
                  topo_lon:units = "degrees_east" ;
          float topo_lat(lat) ;
                  topo_lat:long_name = "ETOPO5 latitude" ;
                  topo_lat:units = "degrees_north" ;
          short topo(lat, lon) ;
                  topo:long_name = "Earth surface topography" ;
                  topo:units = "meters" ;
                  topo:comment = "elevation:positive, bathymetry:negative" ;
  
  // global attributes:
                  :title = "ETOPO5 Earth Surface Topography Data Set" ;
                  :comment = "five_minute resolution" ;
                  :name = "etopo5.nc" ;
  
  or
  
  netcdf etopo2 {
  dimensions:
          lon = 10800 ;
          lat = 5400 ;
  variables:
          float topo_lon(lon) ;
                  topo_lon:long_name = "ETOPO2 longitude" ;
                  topo_lon:units = "degrees_east" ;
          float topo_lat(lat) ;
                  topo_lat:long_name = "ETOPO2 latitude" ;
                  topo_lat:units = "degrees_north" ;
          float topo(lat, lon) ;
                  topo:long_name = "Earth surface topography" ;
                  topo:units = "meters" ;
                  topo:comment = "elevation:positive, bathymetry:negative" ;
  
  // global attributes:
                  :title = "ETOPO2 v2 Earth Surface Topography Data Set" ;
                  :comment = "two_minute resolution" ;
                  :name = "etopo2.nc" ;
  

• Added get_bath.m to extract bathymetry from a NetCDF as a function. It is similar to extract_bath.m driver but in function format. For example,

    [lon,lat,h]=get_bath(Llon,Rlon,Blat,Tlat,OutFile,InpFile)