IMPORTANT: Updated Matlab scripts for nesting

[arango]

Several Matlab scripts were updated for nesting applications:

• grid/grid_connections.m: updated script to support more than one nested grid. The new logic is more robust. There were instances in the double loop logic:

  for dg=1:S.Ngrids,
    for rg=1:S.Ngrids,
      ...
    end
  end
  

  that do not lead to a valid contact region. The new logic is now generic and allows more than two grids.

• grid/grids_structure.m: new function to compute a nested grids structure array, say G(:), containing all the grid variables associated with the application's horizontal and vertical grids. For example:

  G = grids_structure({'my_his_coarse.nc', 'my_his_fine1.nc', 'my_his_fine2.nc'});
  

• grid/contact.m: added logic to process grids without the curvilinear metrics dndx and dmde. The curvilinear switch from the ROMS grid structure G (generated by get_roms_grid) is used process such non-curvilinear applications.

• c_contact.m: corrected bug in the definition of output NetCDF variables: coincident, composite, mosaic, and refinement. They need to be of the size Ncontact instead of Ngrids.

• fine2coarse.m: added logic to process grids without the curvilinear metrics dndx and dmde.

• coarse2fine.m: added logic to process grids without the curvilinear metrics dndx and dmde. The interpolation of the bathymetry, h and hraw, is linear instead of natural to insure that the global integral of bathymetry is conserved.

• grid/write_contact.m: corrected bug during the writing of NetCDF variables: coincident, composite, mosaic, and refinement. They need to be of the size Ncontact instead of Ngrids. The vertical intepolation variable switch is written as true, interpolation(:)=1.

• grid/grid_metric.m: insure that dndx and dmde is zero in non-curvilinear applications.