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Re-assigning land to ocean is complicated process because it requires setting land points to ocean, which then must be initialized. The ocean requires that all points be initialized at start up. If you configure your experiment as a startup run, the new ocean cells will automatically be filled with Levitus (Levitus et al., 1998, Steel et al., 2001) values. However, it is generally desirable to initialize the ocean from a branch or hybrid control experiment, because of the long time scales required to spin up the deep ocean. In order to use a previous ocean restart file, you will need to modify the ocean source code to initialize the temperature and salinity fields for the new ocean cells. This process can be complex and is beyond the scope of this document.
Changing ocean points to land is more straightforward than removing land points, but it still requires multiple steps.
The NCL script change_kmt.ncl remaps ocean points to land to simulate changes in sea level. It may be used in a very simply way to remove the ocean cells representing Hudson Bay. Or you may use your own topography input file to change ocean points to land globally (e.g., to extend the continental margins for sea level lowstands) (Figure 3). The NCL code requires the default binary CCSM3 topography (KMT) and region mask files as input, and produces two new binary files with the user-defined changes to the ocean map. The new binary files are used by the ocean model (pop.buildnml_prestage.csh) and are input to the paleo tool, mk_remap.csh, to create new coupler mapping files that map the new land/ocean map to the atmosphere. Note that the new binary files must be written in big-Endian binary format.
Hint: Check the region mask to be sure you have not eliminated any ocean regions. Eliminating ocean regions requires renumbering the ocean region in the region mask file and changing the region_ids file (e.g., gx1v3_region_ids) correspondingly. By retaining at least one active ocean cell in the default regions, you can avoid having to change the region_ids.
Hint: The NCL code we provide is a template for making macro changes to the default binary KMT map. For best ocean model results, carefully examine your new KMT ocean/land mask for newly emergent islands in the Pacific, open closed basins or change your marginal seas, and widen or eliminate narrow channels. These changes will require hand-editing of the change_kmt.ncl code to fix these problems. We recommend using ncview on the netCDF output file from change_kmt.ncl to identify cells you would like to modify.